Though I feel the same way about not being to link Obito and Tobi as the same person, I disagree about Kishi deciding on Tobi's identity at the last second.
1. We never really saw Obito dying. His last scene had the rocks falling upon him, that was it. Another thing that makes Obito's death a lot different from every other character is that he died with regret, with no closure or anything. The only thing that should've been explained better was how the hell he could survive something like that, but it might be revealed in the future.
2. Kakashi and Obito's Kamui are similar, the pattern of the spirals are pretty much identical.
3. tobitobitobitobitobitobi
4. Kishi loves the dramatic concept of friend versus friend. Haven't you noticed that each generation now has a hero and a villain that knew each other? Hashirama and Madara, Hiruzen and Danzo (debatable), Jiraiya and Orochimaru, Kakashi and Obito, Naruto and Sasuke. The latter three follows the pattern of the good guy and the bad guy being good friends.
5. Kakashi's past and what happened to Rin have been a mystery for ages. If Obito being Tobi was a last minute call, then it wouldn't make sense for Kishi to keep that a secret for so long, or even start a mystery about it.