Offroad, I've rode 26" and 29" tired bikes back to back. At 5'7", I like 26" tire mtn bikes better, offroad. The 29r didn't suck, but I just felt more comfortable and in control with the smaller-wheeled bike. For me, I think it was all about geometry and moment of intertia -- steering and being able to spin the smaller wheels up quicker.

On-road. commuting, I'd not use mtn tires. Period. Another touted benefit of 29r tires is larger (longer) contact patch -- riding on road with knobbies, I imagine this translates into even more resistance.

With current crop of 29r bikes, you usually get a lockout on the fork, so if you need "One Bike to Rule Them All", a 29r would be a perfectly adequate, albeit heavy commuter with just a swap to smoother, hybrid tires. Otherwise, get what bike you want for offroad and stick with something made for the road to commute with.

I like 26" wheels -- next mtn bike I build will have them; current drop bar commuter has them. Lots of tire choices.