Sir Derp Obito has a great theory on how the Rikkudou Sennin was an Uzumaki, one that I agree with almost without reservation. This would seem to support the idea that Naruto is simply the reincarnation of the sage rather than Naruto and Sasuke following the Elder/Younger son parallel. However, I think that this is slightly misguided and that both Naruto and Sasuke have are of the lineage of Senju/Uzumaki and Uchiha/Uzumaki respectively giving them both a means to achieve the true powers of the Sage's legacy and ending the cycle of hatred.
Uzumaki
As stated above Derp has a great thread regarding the Uzumaki and their powers including rikkudou related seals and so forth, but there are a couple of things that I would like to add.
The most important thing is that it seems that the Uzumaki to some degree have the powers of both the Uchiha and the Senju.
This panel shows that the Senju and their relatives were supposed to have strong life force and physical energy, while the Uchiha had strong chakra and physical energy.
This middle panel shows that the Kushina in particular had strong chakra over ala the Uchiha
The middle left panel shows the the strong life force of the younger son in the Uzumaki.
This simply indicates that the Uzumaki have a portion of both powers which will be important later.
Lineage of Naruto
We know that Naruto must be and Uzumaki as his mother is a confirmed Uzumaki, so it is only necessary to show that he has some relation to the Senju and this must come through His father Minato.
We have had many hints that support the idea that Minato is indeed related to the Senju. The first being comparison to Tobirama, and the the second and most compelling being Minato's used of Bijuu mode.
Comparison to Tobirama
We all know that in addition to looking quite similar Minato and Tobirama had a similar array of techniques.
vs
and also
vs.
Though these similarities do not prove that Minato is a decedent of Tobirama or the Senju, we do know that jutsu tend to run in the family. See Tsunade and and Mito with the In seal for byakugou.
Kyuubi Mode
The real evidence for Minato being a Senju comes from both his and his son's seemingly inexplicable used of Kyuubi mode.
When Naruto first revealed Kyuubi mode many people were confused as to why he did not look like any other jinchuriki. Some posited that this was due to Naruto's special 4 tetragram seal, and others due to the fact that he was an Uzumaki, but neither of these can be true as Minato is neither and Uzumaki and he has a different dead demon seal.
Many people were also confused as to how Minato knew that he could use KM as a edo so easily when he never had the Kyuubi chakra in life.
First let's take a look at the conversation that Jiraiya had with the key to Naruto's Seal.
In this conversation Jiraiya is perplexed as to why someone would seal something as dangerous and wild as the kyuubi into their own child. He knows that Minato must have had a very specific reason for doing this he just doesn't know what it is.
Unsurprisingly, when Naruto meet's Minato during the pain fight he asks the exact same question. Why would you seal the Kyuubi in your own son? Minato has an interesting answer to this.
Minato clearly states that the mere fact that Naruto is his son means that he should be able to control half of the kyuubi's chakra. Note that he didn't say that it was because he was Kushina's son, nor was it because he believed in him, but just because Naruto is his son. This leads me to understand that Minato new that the ability to control the Kyuubi's chakra was genetic and that he should have passed that trait on to his son.
This leads to two more questions.
1) If Minato has a genetic affinity for controling the kyuubi and gaining BM/KCM which clan did it come from?
2) Even if Minato had this affinity how would be know about it if he was not the kyuubi's jinchuuriki.
The answer to the first seems pretty straightforward, we have every indication that if this is a genetic trait then it comes from the Senju lineage.
First we see that the aesthetics of KM/BM are very similar to those of the Rikudou Sennin as seen below, indicating a link, possibly genetic through these two via the Senju Clan.
vs.
we also have the serval comparisons between the hiraishin of Minato and that of Tomirama which lends credence to they idea that they are both a part of the Senju can. Not that neither of these thinks are conclusive but together I think they paint a pretty clear picture.
The answer to the second question more directly relates to how Minato stumbled upon KM/BM when he was alive and before he had the kyuubi's yin chakra.
First we know that Minato was married to Kushina who was the jinchuriki of the kyuubi when Minato was alive. We also know that Minato must have done extensive experiments with the kyuubi's chakra while he was alive.
Here we see that Minato had observe the bijuu to create his signature technique the rasengan.
Here we see that Minato had devised "that jutsu" for Naruto to complete using the kyuubi chakra which means he must have had access to the kyuubi chakra in life in order to devise the jutsu.
This still leaves the question of how Minato actually had physical access to the kyuubi chakra if he was not the jin, and I think that this too has been answered in recent chapters.
Here we see that like Kushina, Naruto has the ability to interface with the Kyuubi's chakra and like Minato he has the ability to pass it out to people. So I think the underlying answer is simple Minato used his chakra transferring abilities to access the Kyuubi's chakra through Kushina where he discovered his Senju affinity for KCM/BM.
This indicates that Minato was probably a Senju and that therefore Naruto is Uzumaki/Senju
Sasuke's Power
It is much more difficult to prove that Sasuke is related to the Uzumaki in addition to being an Uchiha as we have had far fewer words spend on his parentage, but if we look at some of the words that tobi had for Sasuke we see that he is indeed special in some way.
Many people may have forgotten this panel as it is more or less impossible now.
The first two panels show that Obito expects Sasuke to surpass a rinnegan user, implying that he can awaken the rinnegan, and sync to the gedo mazo both of which require "Senju" DNA.
Indicating that you need the Senju DNA to control the Mazo like Obito wanted. This panel also shows something else important to determining Sasuke's lineage, that you need Senju and Uchiha powers to awaken the rinnegan. This may seem trivial, but it seems that Itachi wanted Sasuke to awaken the rinnegan when he informed him about the EMS.
The middle right panel is also a controversial one as it indicates that there was a new Doujutsu associated with the EMS, but now that we know that Madara did awaken a new doujutsu i.e. the rinnegan after awakening the EMS and getting Senju DNA we can conclude that Itachi was speaking of the rinnegan here rather than some new EMS jutsu. I therefore think that Itachi was aware of the brother's possible Uzumaki heritage and expected Sasuke to awaken the rinnegan after his eyes were exchanged.
This is reinforced by the following panel.
Itachi says that he want's Sasuke to gain "true power" in the EMS, though he was seemingly aware of the means to awaken the rinnegan which as the eye of the sage and a level above the EMS would constitute true power. I therefore think that Itachi believed that Sasuke would achieve the true power i.e. the Rinnegan upon awakening the EMS, but why didn't he? For the same reason that Madara didn't initially, there is another requirement to awaken the rinnegan, and that requirement is sage mode.
We know that the other requirement that Madara meet when he when he was near death.
This is interesting because we have also seen death as a requirement for a specific type of jutsu in two other cases Senjutsu, and the curse seal.
and
It is important to know that in these cases death is not really required just staying still for an extended period of time in a tranquil state to absorb natural energy.
We also know that the curse seal is just a form of sage mode, and one that Sasuke has/had access to I might add.
finally we got confirmation a while ago that Hashirama had Sage Mode and thus his DNA should allow one to acquire Sage Mode should that meet the requirements of "death" as Madara did.
I therefore find it very plausible that it may not necessarily be "death" that is required to awaken the rinnegan, nor even Senju DNA own it's own. Rather sage mode, which may have Senju/Uzumaki DNA as a requirement, and the EMS are the true requirement. Therefore it Sasuke were to have Uzumaki DNA it would explain his computability with the curse seal, and why Orochimaru was so interested in Sage Mode and the Curse seal and why he was so keen on having Sasuke as a body.
Conclusions
Kishi mentioned that he see's the progress of Naruto and Sasuke as mirror images of one another, and that when one get's a power-up the other must as well. I think that these revelations elucidate the equal trajectory of Naruto and Sasuke's past and future power ups.
Base Level
Naruto = Sasuke
Sage Level
SM Naruto = CS2 Sasuke
Mastering Potential Level
KM Naruto = MS Sasuke
Surpassing predecessors level
BM Naruto = EMS Sasuke (Assuming PS)
SOT6P level
Bijuu Sage Naruto + 9 bijuu power = Dragon Sage Mode Sasuke + Rinnegan
TLDR
Both Naruto and Sasuke have the power of Senju or Uchiha and Uzumaki allowing them to reach RS levels of power while still representing the younger and elder son.
We can tell that Naruto has Senju DNA from Minato, and while it's harder to find evidence for Sasuke having Uzumaki DNA it seems to be implied based on his expected power ups by both Tobi and Itachi.
I had a lot more that I wanted to add to make this theory more credible, but I think that it is already too long so I'll probably add more later, especially to the Sasuke section. I why I think that he has the blood of the Uzumaki rather than that of the Senju.
Uzumaki
As stated above Derp has a great thread regarding the Uzumaki and their powers including rikkudou related seals and so forth, but there are a couple of things that I would like to add.
The most important thing is that it seems that the Uzumaki to some degree have the powers of both the Uchiha and the Senju.
You must be registered for see images
This panel shows that the Senju and their relatives were supposed to have strong life force and physical energy, while the Uchiha had strong chakra and physical energy.
You must be registered for see images
This middle panel shows that the Kushina in particular had strong chakra over ala the Uchiha
You must be registered for see images
The middle left panel shows the the strong life force of the younger son in the Uzumaki.
This simply indicates that the Uzumaki have a portion of both powers which will be important later.
Lineage of Naruto
We know that Naruto must be and Uzumaki as his mother is a confirmed Uzumaki, so it is only necessary to show that he has some relation to the Senju and this must come through His father Minato.
We have had many hints that support the idea that Minato is indeed related to the Senju. The first being comparison to Tobirama, and the the second and most compelling being Minato's used of Bijuu mode.
Comparison to Tobirama
We all know that in addition to looking quite similar Minato and Tobirama had a similar array of techniques.
You must be registered for see images
You must be registered for see images
and also
You must be registered for see images
You must be registered for see images
Though these similarities do not prove that Minato is a decedent of Tobirama or the Senju, we do know that jutsu tend to run in the family. See Tsunade and and Mito with the In seal for byakugou.
Kyuubi Mode
The real evidence for Minato being a Senju comes from both his and his son's seemingly inexplicable used of Kyuubi mode.
When Naruto first revealed Kyuubi mode many people were confused as to why he did not look like any other jinchuriki. Some posited that this was due to Naruto's special 4 tetragram seal, and others due to the fact that he was an Uzumaki, but neither of these can be true as Minato is neither and Uzumaki and he has a different dead demon seal.
Many people were also confused as to how Minato knew that he could use KM as a edo so easily when he never had the Kyuubi chakra in life.
First let's take a look at the conversation that Jiraiya had with the key to Naruto's Seal.
You must be registered for see images
In this conversation Jiraiya is perplexed as to why someone would seal something as dangerous and wild as the kyuubi into their own child. He knows that Minato must have had a very specific reason for doing this he just doesn't know what it is.
Unsurprisingly, when Naruto meet's Minato during the pain fight he asks the exact same question. Why would you seal the Kyuubi in your own son? Minato has an interesting answer to this.
You must be registered for see images
Minato clearly states that the mere fact that Naruto is his son means that he should be able to control half of the kyuubi's chakra. Note that he didn't say that it was because he was Kushina's son, nor was it because he believed in him, but just because Naruto is his son. This leads me to understand that Minato new that the ability to control the Kyuubi's chakra was genetic and that he should have passed that trait on to his son.
This leads to two more questions.
1) If Minato has a genetic affinity for controling the kyuubi and gaining BM/KCM which clan did it come from?
2) Even if Minato had this affinity how would be know about it if he was not the kyuubi's jinchuuriki.
The answer to the first seems pretty straightforward, we have every indication that if this is a genetic trait then it comes from the Senju lineage.
First we see that the aesthetics of KM/BM are very similar to those of the Rikudou Sennin as seen below, indicating a link, possibly genetic through these two via the Senju Clan.
You must be registered for see images
vs.
You must be registered for see images
we also have the serval comparisons between the hiraishin of Minato and that of Tomirama which lends credence to they idea that they are both a part of the Senju can. Not that neither of these thinks are conclusive but together I think they paint a pretty clear picture.
The answer to the second question more directly relates to how Minato stumbled upon KM/BM when he was alive and before he had the kyuubi's yin chakra.
First we know that Minato was married to Kushina who was the jinchuriki of the kyuubi when Minato was alive. We also know that Minato must have done extensive experiments with the kyuubi's chakra while he was alive.
You must be registered for see images
You must be registered for see images
This still leaves the question of how Minato actually had physical access to the kyuubi chakra if he was not the jin, and I think that this too has been answered in recent chapters.
You must be registered for see images
Here we see that like Kushina, Naruto has the ability to interface with the Kyuubi's chakra and like Minato he has the ability to pass it out to people. So I think the underlying answer is simple Minato used his chakra transferring abilities to access the Kyuubi's chakra through Kushina where he discovered his Senju affinity for KCM/BM.
This indicates that Minato was probably a Senju and that therefore Naruto is Uzumaki/Senju
Sasuke's Power
It is much more difficult to prove that Sasuke is related to the Uzumaki in addition to being an Uchiha as we have had far fewer words spend on his parentage, but if we look at some of the words that tobi had for Sasuke we see that he is indeed special in some way.
Many people may have forgotten this panel as it is more or less impossible now.
You must be registered for see images
The first two panels show that Obito expects Sasuke to surpass a rinnegan user, implying that he can awaken the rinnegan, and sync to the gedo mazo both of which require "Senju" DNA.
[/IMG]http://178.21.19.200/manga/mangas/Naruto/606%20-%20Dream%20World/15.jpg[/IMG]
Indicating that you need the Senju DNA to control the Mazo like Obito wanted. This panel also shows something else important to determining Sasuke's lineage, that you need Senju and Uchiha powers to awaken the rinnegan. This may seem trivial, but it seems that Itachi wanted Sasuke to awaken the rinnegan when he informed him about the EMS.
You must be registered for see images
The middle right panel is also a controversial one as it indicates that there was a new Doujutsu associated with the EMS, but now that we know that Madara did awaken a new doujutsu i.e. the rinnegan after awakening the EMS and getting Senju DNA we can conclude that Itachi was speaking of the rinnegan here rather than some new EMS jutsu. I therefore think that Itachi was aware of the brother's possible Uzumaki heritage and expected Sasuke to awaken the rinnegan after his eyes were exchanged.
This is reinforced by the following panel.
You must be registered for see images
Itachi says that he want's Sasuke to gain "true power" in the EMS, though he was seemingly aware of the means to awaken the rinnegan which as the eye of the sage and a level above the EMS would constitute true power. I therefore think that Itachi believed that Sasuke would achieve the true power i.e. the Rinnegan upon awakening the EMS, but why didn't he? For the same reason that Madara didn't initially, there is another requirement to awaken the rinnegan, and that requirement is sage mode.
We know that the other requirement that Madara meet when he when he was near death.
You must be registered for see images
This is interesting because we have also seen death as a requirement for a specific type of jutsu in two other cases Senjutsu, and the curse seal.
You must be registered for see images
and
You must be registered for see images
You must be registered for see images
It is important to know that in these cases death is not really required just staying still for an extended period of time in a tranquil state to absorb natural energy.
We also know that the curse seal is just a form of sage mode, and one that Sasuke has/had access to I might add.
You must be registered for see images
finally we got confirmation a while ago that Hashirama had Sage Mode and thus his DNA should allow one to acquire Sage Mode should that meet the requirements of "death" as Madara did.
You must be registered for see images
I therefore find it very plausible that it may not necessarily be "death" that is required to awaken the rinnegan, nor even Senju DNA own it's own. Rather sage mode, which may have Senju/Uzumaki DNA as a requirement, and the EMS are the true requirement. Therefore it Sasuke were to have Uzumaki DNA it would explain his computability with the curse seal, and why Orochimaru was so interested in Sage Mode and the Curse seal and why he was so keen on having Sasuke as a body.
Conclusions
Kishi mentioned that he see's the progress of Naruto and Sasuke as mirror images of one another, and that when one get's a power-up the other must as well. I think that these revelations elucidate the equal trajectory of Naruto and Sasuke's past and future power ups.
Base Level
Naruto = Sasuke
Sage Level
SM Naruto = CS2 Sasuke
Mastering Potential Level
KM Naruto = MS Sasuke
Surpassing predecessors level
BM Naruto = EMS Sasuke (Assuming PS)
SOT6P level
Bijuu Sage Naruto + 9 bijuu power = Dragon Sage Mode Sasuke + Rinnegan
TLDR
Both Naruto and Sasuke have the power of Senju or Uchiha and Uzumaki allowing them to reach RS levels of power while still representing the younger and elder son.
We can tell that Naruto has Senju DNA from Minato, and while it's harder to find evidence for Sasuke having Uzumaki DNA it seems to be implied based on his expected power ups by both Tobi and Itachi.
I had a lot more that I wanted to add to make this theory more credible, but I think that it is already too long so I'll probably add more later, especially to the Sasuke section. I why I think that he has the blood of the Uzumaki rather than that of the Senju.