The point is, essentially, if you take a 26" wheelset w/ the same exact number of spokes, in the same gauge, with the same extrusion for the wheels (say, sun mtx33 26" vs sun mtx33 29"), same hubs, same tires (say, nevegal 26x2.2" vs nevegal 29x2.2"), the 29 wheels/tires are going to weigh more. And, it's rotational weight, which is going to count for a lot more than dead weight. (Flipside: those bigger wheels will hold momentum longer; get going to like 15mph and coast, all other things being equal, the 29" will roll longer.) Also, the larger diameter wheels with longer spokes will be weaker, all other things being equal. The shimano hubs with upgraded freehub bodies also had modification to the hub flanges for added strength. (I've heard that a lot of shimano freehub bodies die young, even on 26" bikes. I've never had a problem,, but I'm more of a SS guy.)
As for gearing: like I said, I'm a SS guy. so, my usual 32x17 26" SS gearing went to a 32x19 for the 29" SS I used to run. NBD. But, I've read a bunch of articles and forum posts where guys were whining about gear ratios, which led to 29"-specific chainsets with smaller rings and 12-36t "29er" cassettes. With 10speeds taking over, with the 36t low gear being basically standard, that kinda solved itself. Again, NBD, but still one detracting factor(albeit one that's sort of going away).
BITD, early 29ers had awkward geometry and suffered from a lack of awesome rims and rubber variety. Nowadays, that's all gone (except that I suspect the small frames with 29" wheels prolly handle terribly.). But, there are still reasons why I love 26", and it saddens me to see 26" hardtails/rigids dying out. I like the snappy acceleration, the nimble handling, and the bombproof wheels. Still trying to figure out what my next mtb will be, and I may go with a 29er again... but I suspect I'll pick up a 26".