Well if you can't find it logical how can Obito be Tobi, there isn't any problem in the chronological order but I won't go into details because right now I'm too lazy. As for ruining his character, it didn't, in fact quite the contrary. No one likes a villain who does all he does just because for the cliche of conquering the world. By making the good into the bad one it gives a realistic element to the story. People don't always stay as they are, they changed based on the hardships they go through. Also, you say that Obito's change is a bit biased, well not really. Obito was a guy who sacrificed himself to save his teamate and went even as far as to give him his sharingan to pretect the one he loved. Then he stayed for months alone with Madara, who had a very twisted character and despite that he sticks to his ways only to witness later with his own eyes the death of her loved one by the hand of the man, she loved and to whom Obito had entrusted his eye to protect her. I think that's quite enough to become crazy.
For that reason I really like Obito, he's my second favourite after Naruto. He's a perfect anti-hero who used to have the same ideals Naruto has and yet we see him how much his minc has now twisted becoming a fallen sage of six paths and getting the biggest power that ever existed. But the reason I like him most of all is because he's not a victim. In contrast to other characters like Nagato, Obito knows full well that can't trust others like Madara and even goes as far as to trick the man who saved his life, even if he did it for his own reasons showing just how clever Obito was since he was a kid.
He's not just another naif guy. He knows what he wants and is there to get it:cool
Also here is a quote from when he was a good guy: (To Kakashi) "Those who break the rules are trash, but those who abandon their comrades are worse than trash! If I'm going to be called trash either way, I'd rather break the rules! And if that somehow makes me anything less than a real shinobi, then I'll crush all of the so-called "real" shinobi!"
He always had a specific philosophy, just the way things turned, strenghtened his opinion.