I have been riding my 29er (raleigh xxix, rigid ss) for a few months now. For me, there are a couple tight switchbacks I barely made on my 26 (geared ibis mojo) that I don't always make on the 29er. So, for me, a little less able to make the tight switchbacks. That said, others remarked that the tight switchbacks don't bother them, so it could just be me.
I did feel that I couldn't accelerate as well, especially during a technical climb. Then, I got a much lighter wheelset, and most of that is now gone. And the positive things far outweigh the small negatives. If Ibis makes a 29er Mojo, I'll sell my 26er immediately and buy it. But, I still love the mojo for the rough stuff, the rigid ss 29er for everything else.