That's what I've got aswell I've got my trail bike with 2 sets of wheels, one with thin slippery road tyres for commuting and one with trail tyres on them........... Then I've got my DH rig with some highroller supertackys !
If you are looking for a bike for general commuting and some cross country the 29" rims will help you out, but if you are looking at progressing and hanging of the sides of the bike, jumping it and drifting on hard pack / chucking the bike about 26" is the way to go. Obviously frame choice will dictate the ability to that kind of thing aswell, Saying that though if you do progress you will probably be looking at upgrading the bike anyway.