I still get the strange feeling that Tobi is Fugaku, but in addition to this there is a link between him and Izuna/Madara, possibly one of them being his father. It has been foreshadowed throughout the entire series that Fugaku is a suspicious character, especially in his behaviour towards Itachi and Sasuke. My theory is a bit far-fetched, but Fugaku, after falling out with Itachi, and after seeing his other son's mastery of the fireball jutsu, realized that Sasuke would be the appropriate one to succeed him(the reason why he has been nurturing him for so long
My own reasons for it having to be him.
For instance his name:
The name "Fugaku" is an alias, or alternative name, for Mt. Fuji in Japan. While the origin for Mt. Fuji's name isn't 100% clear, a Japanese text says it gained its name from the word "immortal" (Fuji). Tobi is called immortal by many characters in Naruto.
Another origin of the name of Mt. Fuji says that it gained its name from an idea of "an abundance (fu) of soldiers (shi/ji)". Tobi has 100,000 soldiers at his bidding.
Another Japanese folklore says that Fuji came from the words "not" and "two". In Japan, this translates as "without equal" or "having no equal". That would explain his character as the main antagonist.
For appearances, when Tobi removed his mask, it was clear that the man is aged and has 2 bags under his eyes. If you look closer, there's also Fugaku's and Itachi's prominent facial creases. Fugaku was 40 at his apparent death. The story has since moved on 10 years, giving an appropriate age for the man under the mask.
remember also that Tobi went out of his way to make sure Danzo died. Personal Vendetta.
This here is speculation, but when Shisui tried to use Kotoamatsukami on the Uchihas(namely Fugaku, being the leader), he failed after being intercepted by Danzo who stole one of his eyes. This jutsu might have been the only to stop them, but he got away and gave Itachi his remaining eye. This is also why Tobi(Fugaku) was insistent on taking out Danzo, because Shisui's jutsu could oppose him
This by the way is also the reason why Itachi was kept under tabs consistently by Kisame, under direct orders from Tobi(Fugaku). Tobi acted like a buffoon when Itachi was alive. A ploy to hide his real manerism from him. As soon as itachi died. Tobi began to act normal.
Fugaku needed an alias. His name is not feared and won't gather immediate respect. Thus, he took on "Madara" as both of their ideals are similar. Since their ideals are similar, no one would question if he was really Madara.
Since killing the entire clan would make Itachi a rogue shinobi, this was the perfect opportunity for Itachi to help Fugaku. As a rogue shinobi, he would be hired into Akatsuki, unwillingly helping Fugaku to achieve his master plan.
Another reason is the development of Sasuke. Sasuke had recently become his father's new champion. Knowing that anger can drive a person without end, killing off his clan and family would jump-start a potential powerful shinobi.
He faked his death because the Konoha elders had figured him out and uncovered his plot. They were using Itachi against him. Therefore he effectively removed himself from their sight, and has been biding his time until now to make his move.
remember also that Tobi attempted to reveal himself to Sasuke, knowing he would recognize him, therefore erasing the possibilities of hime being Obito/Madara/Kagami etc. If Sasuke saw Fugaku, he would find solace in the father he tried so hard to make proud and join him in his conquest(AT THAT POINT!!). After the second meeting with Itachi though, Sasuke's views on the world changed, and possibly revealing Tobi's identity to him would turn him on the path to redemption?
Besides
During the 9-Tails' attack, it was revealed that Kushina and Mikoto Uchiha (Sasuke's mother) are friends, and good ones at that. Mikoto was also said to be missing during the 9-Tails' attack. She was noticeably compliant with Fugaku's ideals of the Uchiha taking over. Thus, she told Fugaku of Kushina's pregnancy, giving him the perfect time to release the 9-Tails. That's a connection for their mothers.
Where was Fugaku??? He was fighting Minato!
As for how Fugaku escaped death when itachi went to kill him, there are several explanations.
1. A Zetsu clone was placed in his stead.
2. Genjutsu
3. Obito's ocular power (far-fetched, but sending the part of his body pierced by the sword to the other dimension?)
Either way, Fugaku would manage to escape, giving him the perfect alias so Itachi wouldnt suspect Tobi of being him, and he fled to Kirigakure to start building Akatsuki(Taking control of Yagura).
Possibility:
When he failed to destroy Konoha and the elders, he had to re-think his plan.
What he came up with was the Eye of the Moon Plan. It was then where he decided to gather Hashirama's DNA in order to obtain Izanagi and greater powers. Since these bodily experiments would be rather obvious, he had his reliable servant, Zetsu, make a clone of him before starting. From that day on, it was the Zetsu clone that took his place in Konoha.
If thats the case, then this would kill his Zetsu clone, significant because if left unharmed, the clone would theoretically not age. This would reveal that it's not really Fugaku.
It is also possible that by the time of the meeting, Fugaku may have attained Rinnegan, but explaining such a thing would be quite difficult, that last bit i'm leaving for Kishi.
It would be the best choice in my opinion.
Remember this cycle of hatred has been passed though generations.
Hashirama-Madara
Minato-Fugaku(would be logical)
Naruto-Sasuke
Naruto made a promise to Pain that he would end the cycle of hatred(The plot of the series revolves around this), if not on a world scale then he would start with the Senju-Uchiha one.
Sasuke discovering Fugaku would force him to come to terms with the Uchiha and realize Itachi's wish, which would lead to his return to Konoha
Possible ending: Sasuke joins the fight and defeats his father(Star Wars, but with chakra ninjas), or(in my opinion would be better) tell Naruto to stand down as he redeems the Uchiha's name alone in defeating Fugaku(EPIC). Afterwards they would aid one another in taking down Madara (?), giving Naruto the true impetus to become Hokage(one of the perks being that he could grant a "royal" pardon to Sasuke for his crimes), and possibly have Sasuke become his advisor(?)
this whole idea makes sense also because of the fathers.
For their fathers, they fought during the 9-Tails' attack. One was the Child of Prophecy that potentially could bring world peace, while the other wanted to have world domination, in his own sense of "peace". This clash reverberates in their sons, but the cycle of hatred must end, because Naruto was entrusted this by Jiraiya.
other facts that fit with Tobi being Fugaku.
his insistence on executing Danzo, it's far too prominent(He knew Danzo had Shisui's eye and was worried about it's power.
He is extremely protective of Sasuke,
Fugaku as leader of the Uchiha clan is a master ninja. He trained Itachi. His genetic stock gave birth to two of the greatest ninja talents. There is no way he was some pushover that Itachi could just kill at a whim. He is Tobi.
there is no other explanation why Tobi would turn from acting like a bumbling idiot to a powerful warlord right after he was told by Zetsu that Itachi died!!!! REMEMBER THIS FACT! Itachi's death directly influenced his revealing his true nature, the only explanation is that he is Fugaku, he would have no reason to go around doing this as anyone else
it would be a seriously freaky plot twist if on the night of the Uchiha massacre, Danzo went around collecting eyes in Itachi's wake in an attempt to later enlist Orochimaru in the surgery, but Fugaku was in parallel collecting eyes(We see later that Tobi has a huge collection of Sharingans). This is extremely far-fetched but this is one way of explaining the abundance of eyes in Tobi's possession
this would also lead to the inevitable vendetta against Danzo, wanting the last of the Sharingans to be in his(Tobi's) possession, except for the only ones left that can defy him(Sasuke)
ONCE AGAIN I WILL STATE!!(VERY IMPORTANT)
Tobi recognized Danzo death move as Shisui's sharigan power. How would Tobi know of shisui's power and identity unless he knew him and witnessed that power before(Shisui's attempted Kotoamatsukami against Fugaku repelled by Danzo)
Danzo stopped Shisui because he didnt want some subservient Uchiha under genjutsu, he wanted them DEAD. he did not believe that they would ever cast their hatred aside, so he believed they would inevitably be freed from Kotoamatsukami(what then? hh)
as for Tobi being Obito, timewise it's also strange, it's safe to assume that Nagato is older than Obito, considering the fact that he was Jiraiya's student before him taking on Minato who would far later take on Obito, in that case how could Obito as Tobi ever have given the Rinnegan to Nagato(remember Nagato had it before he met Jiraiya). I think that single-handedly proves Obito is not Tobi, unless according to your theory Madara gave it to Nagato intending to entrust brainwashed Obito with retreiving it, doesnt fit
with Obito its basically all plotholes, you see, with Fugaku it makes for an epic climax and logical conclusion. Besides all of the foreshadowing throughout the series is not there for nothing, everything has a reason, why Hiruzen's wife was angry at Kushina for revealing the date of birth to Mikoto, why Kishi included the scene of Itachi sitting with baby Sasuke wondering where his parents were on the night of the Kyuubi attack, etc. These are simply subtle literary tools
sorry for my rambling, the point might be off and there might be some contradicting comments because this is just a collection of youtube comments I made over the past few days.
Throughout my theory, ponder this: what if kotoamatsukami SUCCEEDED before Danzo took Shisui's eye(on everyone except for Fugaku obviously, remember he did arrive back suspiciously on that same day that Itachi was accused by his clansmen)
