The Zetsu's probably had had enough of working for that deranged pensioner Madara Uchiha, and chose to side with Obito. Obito actually seems like a funny likeable character, a bit like Naruto. The Zetsu's have feelings as well and Obito being a kid, he probably could relate to them more that Madara, who used them as mere tools for his plans.
Madara 'rest's' reminds me a little bit of Apocalypse in his Lazarus Chamber in Xmen. Except with Apoc, he actually was rejuvanated to his full health, but with Madara, it doesn't restore his vitality.
Also, do you guys think Obito knew the location of Madara's body when he 'died' or do you think he hid it from his protege, just in case he got cute? Although Madara is a brilliant mastermind, he does take risks with his life and power. He could have lost both to Hashirama and Nagato forever, so its possible Obito always knew where his body was, hence why he was so shocked Kabuto found it.