I'm not sure the movie ever defines what God wanted - if indeed he "wanted" any particular outcome.   If Noah had killed infants and ended the human race, the God of this movie might have said "huh, interesting" and then started over the next day with sentient crocodiles.  He's God, after all - he can do/undo anything if he chooses to. 

Maybe it's all an experiment without a "right" or "wrong" outcome.  Noah has his take on what it all meant, his wife has another, God doesn't say either way.  In the end, He lets the human race continue - that's the only thing the movie says for sure.

Which, again, is what was so interesting and refreshing to me about this movie, as compared to the standard Hollywood Bible flick.

The closest analog I can think of is - believe me or not - the Schwarzenegger Conan movie, and the climactic scene where Conan "prays" to Crom by saying "Yo, I'ma do this thing now.  I think it's what I should do.  It'd be nice if you helped me, and if you don't then the hell with you."  And then Crom sorta does help maybe a little, or maybe he doesn't actually - the movie never says for sure.  I see the movie of Noah doing pretty much the same thing, and I dig it.

Noah doesn't hear anything, he's given visions he must interpret. But at no point is it a matter of interpretation or ambiguity that the Creator exists and is quite actively engaged in the process.