Here is my 2 cents:
Since tobi=obito is annoying because of major inconsistancies everyone mentionned (I wont list them one more time);
If we wanna try to find an other explanation and if we remember:
- Tobi pouring goo instead of blood
- Tobi claiming he is nobody
- Zetsu being able during the "war" to take appearance and imitate chakra and so on, of anyone he has DNA or at least had contact with (remember Neji and others).
Then we can think, as many stated, that tobi could have a connection to zetsu (being the main zetsu, being a zetsu clone, being a better version of zetsu created by ???, whatever) and that's how he can mindfuck people by appearing as who he wants (as long as he has DNA or whatever Zetsu needs to do that) opposed to mindfuck people with genjutsu as ACT was suggesting.
That would explain different appearances (long hair/short hair, Kisame recognizing madara, chakra recognition etc.)
Still, even though he is just a kind of zetsu taking appearance of Obito to mindfuck kakashi/gai, he still actually had obito's eye for all those years...
I, maybe naively, still think that Kishi knows, in the great scheme, what he is doing and would not make such major decision that would screw his work withtout realizing all the inconsistencies with his own story line.
So hopefully for the sake of his manga, even if not this one he will have some kind of good explanation...