The Heck, Madara?
I think it's safe to say that Mada's motives are unclear as of chapter 638.
I'm pretty sure his motive is the cliche "world domination". Or something like that. If he wanted to continue with the plan, he'd let Obito do whatever he wants, because he knows Obito's goal is initiating the Infinite Tsukyomi.
I fail to see Madara wanting to live in a perfect world right now.