I will say it again Kakashi asked him why he didn't come back to the village, the answer given was .... Cause Rin died.
Now if he asked "why have you become evil and want to do all these things?" then THAT would be be different.
Basically I got out of that he didn't come back because he felt nothing was there for him.
So eventually he ran into Mr. bad Influence Uchiha over there and the rest is a secret history Kishi probably won't have the time to go into completely.
Now the loop holes will hopefully be filled far as When was it Obito and when was it Madara? My guess it was only Obito when he surfaced with Akatski, replacing Orochimaru(so to speak).
How he used his jutsu years before now i don't know.