Sasuke wants to destroy Naruto, because Naruto represents not only all that was historically opposed to the Uchiha, but also the conflict within Sasuke himself. He's always seen a strength in Naruto that he can't match or comprehend, throughout their battles with Orochimaru, Gaara, and Akatsuki. He needs to prove that his way of gaining strength, and his ideology, are stronger than Naruto's.
Now, neither of them may give a damn about the history of the Rikudou's heirs, but Madara does, and he lives for that legend. He's enacting his revenge against his own history of defeats vicariously through Sasuke, and sees in Naruto the perfect representation of all he admired and hated about Hashirama. For that reason, he's attempting to indoctrinate Sasuke fully into his own twisted ideals.
Unfortunately, there's always been a part of Sasuke that was nobler, braver, and more compassionate than Madara ever was, even if Sasuke and the rest of the world have tried their best to take that from him. However, Naruto's always been the one that reminded Sasuke of that, as seen from the start when Sasuke sacrificed himself (and thus his revenge) to save Naruto from Haku. And Madara cannot comprehend that part of Sasuke or Naruto, and can't predict or control it. It's the reason his plans with Nagato were foiled, and why, even now, his control over Sasuke has diminished. Perhaps that's the real reason Madara wants Naruto (and the Senju, etc) to be so completely erased: he's afraid of the Will of Fire.
Now, given how personal this has all been for Madara, it'd be somewhat surprising if Tobi ended up actually being Izuna. We don't know enough about Izuna's backstory, even if he seems likely to share his brother's hate for the Senju and lust for power. He's certainly put a lot of effort into proving that he's Madara for a guy who still wears a mask, but we've never seen any definitive proof.
One does have to wonder, though, why he gripped his arm like that when he explained the "truth" about his brother. It could be that he was lying about the voluntary offering of the eyes. It could be anger towards the death of his brother. It could even be that, in actuality, he IS Izuna, and the memory from his perspective was particularly hard, even for him, to lie about. The details of Izuna's life (and death) are shady at best.
It would add even more depth to the similarities between Tobi and Sasuke if Tobi were, in actuality, Izuna. Imagine, both worshipping their elder brothers, but taking opposite paths: Madara steals Izuna's eyes in lust for power, and pretends that he's protecting his clan from the Senju, while Itachi raises Sasuke to one day take his eyes, destroying his clan to protect the Senju. While Madara gladly sacrifices his brother, Itachi never brings himself to sacrifice his. Sasuke lives his life denying Itachi's sacrifice, and in the end is forced to accept it, while choosing a different path. Izuna chooses instead to tell the lie his brother told, and to finish the job Madara started. In the end, both are fighting to avenge their brothers, no matter the rationale.
It can't be stressed enough the relationship between both sets of Mangekyou brothers. We know all about Madara, Itachi, and Sasuke... but we still know very little about Izuna. Tobi manipulates Sasuke by using the essence of his brotherly love and life of betrayal/illusions against him, but he'll gladly tell more about the Rikudou and his heirs than he will his own flesh and blood, his own eyes. Very suspicious!
Oh, and the eye behind the mask is the same eye we saw Madara take first from Izuna in the flashback. Just putting that out there, even if theories about the mask / eye are years old and somewhat tiresome after Danzou's introduction and death have come and gone.
Again, the Uchiha are a clan shrouded in illusions. Tobi mastered the Uchiha run-no-jutsu far better than Itachi, via his teleport; he's also concealed all truths about him more effectively, thanks to his handy mask.
It's never too late for him to be Obito! Even after he dies at the end of the manga, we can still say, "I bet that was really Obito... rat bastard carried his secrets to the grave..."
Bookmarks