I have a 2008 335i with the same hesitation. I am convinced it is the transmission and not the turbo's or otherwise. There is a lot of talk from other's about it as well all over the E90 boards.

The car hesitation seems to start, from a stop, in second gear. It goes away when the automatic transmission is in sport mode. I either forgot about it, adapted to it or its gotten better as I did not think of it until reading this post.