There are certainly some benefits to the 29 inch wheels over the standard 26 inchers, less rolling friction, more comfortable ride, better obstacle rollover, and even better traction. These are some significant benefits that bike designers are always trying to achieve.
On the other hand, looking at the some of the other current trends in the industry, 29 inch wheels are headed in the opposite direction. They have more rotating mass, they certainly aren't lighter, they have a higher center of gravity(just slightly), and designing a 29 inch bike with more than XC travel can pose some serious problems.
Furthermore, for those of us who aren't exactly tall, 29 inch bikes can require some sacrifices such as higher headset/handlebar height, and longer top tubes. Because of this, we will also find a smaller selection of models to choose from.
An interesting fact that proponents of the 29 inch trend like to point out is that the 26" wheel standard has somewhat arbitrarily beginnings. This is true. The 26" wheels and tires used in the early days were simply used because that was a convenient size found on adult and cruiser bikes of the time. However, using this as an argument in support of 29" wheels downplays the fact that those 26" wheels of the day were that size for already good reasons.
I think by far, the biggest argument against the 29 inch category is that it creates some issues with longer suspension travel and it seems that is the way the industry is moving these days.
Some will argue that because of the bigger wheels, not as much suspension is needed, but this only applies to certain circumstances and only to a certain level.
On the other hand, 29 inch mountain bikes are creating some undeniable benefits. For larger to normal sized people who know they don't want more than XC travel (80mm-100mm), these bikes may have some serious merit.
I don't think the debate over Wheel size is going to go away anytime soon. There is no reason why there won't be room for both 26 and 29 inch wheels in the future, or any other size for that matter.
The real trick here is finding a bike that works for you. If it has 29 inch wheels, great.
Either way, 29 inch bikes deserve some credit. Questioning the norm is never really a bad idea.
29 inch bike technology is improving every season. It's fun to watch the new trends.