I think it is just a case of the story just taking a life of it's own. I don't think he had Obito planned out that far ahead. More likely it was somewhere closer to around Kakashi Garden, or quite possibly at the start of the time skip. But I do think he had at least some type of connection planned between Minato's and Kakashi's planned back then he just may not have been exactly sure where he wanted to go with it at the time.
I believe that Kishi always planned Obito to be Tobi. However, because of the amount of people who were able to deduce his identity he tried to troll us with the whole claiming to be Madara Uchiha. I don't think Kishi intended Obito to be the mastermind behind akatsuki.
Kishi did a lot of plot hole filling just before and after Obito was revealed to be Tobi, in order to make that idea work. In fact there are still some plot holes left unfilled. That always gave me the impression that it wasn't planned too far ahead.
Edit: I think Kishi chose Obito because it would be the most controversial option, and controversy sells manga.
I don't understand why people think kishi just adds and modifies the story along the way.. from day one he started naruto he had the big picture in his mind until the last chapter which still has to come.