26" will be more responsive, a little faster to accelerate, little rougher ride. Although, I've run 26x1.8 to race on hard pack, and they were pretty fast.
29" smoother ride, you can roll over more, and once you get them going, its easier to keep them rolling. Descending is a lot better too. You can't throw the bike in and out of turns as well as a 26" bike, but you get that back in being more efficient on rollers/flats.
As far as climbing goes, seems to be six of one, half dozen of the other to me. I noticed a big performance difference when I started running Stan's NoTubes 29" wheels.
Al Painter, NASM CES, PES, BA
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