This is more of a fun theory, and none of it is meant to be taken very seriously. Here is just some random points of evidence, and this is for complete fun 
Ninja are getting Weaker:
Sage of Six Paths > Uchiha Clan Ancestor and Senju Clan Ancestor > Madara and Hashirama > Obito, Nagato and Minato > Prime Sannin / Sasuke and Naruto
Notice how the 'weaker' ninjas are almost always the newer ones? xd It's probably because there are less wars and ninjas are getting weaker because such strength isn't needed.
Rinnegan, Sharingan, Byukugan:
This one can be taken seriously if you want. Rinnegan appeared in the ninja evolution because the ninja population would have been wiped out by Juubi. After the Sage of Six Paths the Rinnegan wasn't needed again (until now) because Juubi was gone, but there are some things evolution can't remove permanently (eg. tail bone segment from our ancestors) so Dojutsu remained. There were two offshoots of this; the Sharingan which took over the Ninjutsu and Genjutsu parts of the Rinnegan and developed its own, while Byukugan is the taijutsu offshoot. That is why other than Madara none of the characters Sharingan 'evolved' into the Rinnegan; evolution won't let useless stuff happen for the most part. It's possible that Madara awakened the Rinnegan, not because of the Senju DNA but more specifically Hashi's DNA. We knew Hashi came across almost all if not all of the Tailed Beasts. This may have left a mark on his DNA similar to the Juubi and because of this the EMS (d)evolved.
That is all
Hope you enjoyed 
Ninja are getting Weaker:
Sage of Six Paths > Uchiha Clan Ancestor and Senju Clan Ancestor > Madara and Hashirama > Obito, Nagato and Minato > Prime Sannin / Sasuke and Naruto
Notice how the 'weaker' ninjas are almost always the newer ones? xd It's probably because there are less wars and ninjas are getting weaker because such strength isn't needed.
Rinnegan, Sharingan, Byukugan:
This one can be taken seriously if you want. Rinnegan appeared in the ninja evolution because the ninja population would have been wiped out by Juubi. After the Sage of Six Paths the Rinnegan wasn't needed again (until now) because Juubi was gone, but there are some things evolution can't remove permanently (eg. tail bone segment from our ancestors) so Dojutsu remained. There were two offshoots of this; the Sharingan which took over the Ninjutsu and Genjutsu parts of the Rinnegan and developed its own, while Byukugan is the taijutsu offshoot. That is why other than Madara none of the characters Sharingan 'evolved' into the Rinnegan; evolution won't let useless stuff happen for the most part. It's possible that Madara awakened the Rinnegan, not because of the Senju DNA but more specifically Hashi's DNA. We knew Hashi came across almost all if not all of the Tailed Beasts. This may have left a mark on his DNA similar to the Juubi and because of this the EMS (d)evolved.
That is all