If your bike doesn't fit you (frame size, saddle height, reach, etc., it's not going to be comfortable, and you're not going to like it very much.
I'm not one of the cool kids, but I do have both a Fisher 29er and a 26" Specialized hardtail, and I much prefer the 29er. I'm not a real technical MTB rider -- mostly cross country, and I can go places and cross obstacles and seemingly bottomless pits with my 29er where the 26" would have me dead in a ditch somewheres. As Emily notes, if the frame fits you, it doesn't matter much how big the wheels are.
That being said, the 29er wheels take a little more motor, or oomph to get them rolling, but once you do it's not a lot of extra effort to keep your momentum. And I like the ability to pretty much float over most anything that gets in my way.
Depending on your riding style, you'll probably like it if you try the big wheels. I know I wish I'd listened to Odell over at the bike shop when he tried to guide me over to the 29er rack when I first took up MTBing....





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