There's an awful lot of material that suggests that he was always meant to be Obito, from the very beginning. Which is precisely the problem.
Thing is, it's not certain whether...
1. Kishi was just poor at making a plot twist. He put so much evidence in the story that it became so damn obvious it was Obito by chapter 599. He could have held back on some of the info he gave us, creating a much bigger reveal.
2. Kishi is just ridiculously clever, putting so much evidence in front of us that he actually created a double bluff, forcing fans to try and justify ways in which it couldn't be Obito (because it was so obvious), and then actually revealing it to be Obito in the end. The problem with this tactic is that it doesn't really have a "wow, that's actually really clever" factor, and by the time you get to chapter 599, it's just annoying.
Don't get me wrong, as a character, the fact that Tobi is Obito is good, given the dramatic effect it has on Kakashi, Naruto etc...however it's just the process by which Kishi chose to bring him into the story that could have been better. Plus, his whole philosophy and monologues he's coming up with right now is just screaming for a TNJ, so I hope Kishi does something different this time