For me they have different purposes. I don't feel as comfortable on my 29er on super technical descents as I did on my 26", possibly because I'm now on a 20# race bike, however, almost everything I ride up and down, I'm faster on.
The places where 26 suit me better are when there are hairy drops to be taken, as well as extremely rocky, ledgy, technical sections that require a lot of trials type maneuvers.
The next bike in the stable will probably be a stumpjumper evo with a lyric on it, maybe a blur lt or a nomad. I'll be using those to supplement the 29er.
I have found that I look harder now for rear tire characteristics. Specifically, where I ride, I'm looking for a much meatier front tire than rear tire, so I can skid the rear around corners. This at speed is typically faster than I used to take stuff.
My previous boss is the texas 40+ master's state champ. He switches between 29 hardtail and 26 full suspension depending on what he feels like. Wheel size don't keep him from winning.
Being vertically challenged
5' 5", I found that I have had to go for a -20 stem to drop the front end to allow me to get my weight over the front. I have just bought a Stumpjumper Evo (26") and love it. Not something which you could race XC though due to the weight penalty.