Okay, I've skimmed the other opinions, and now I'll offer mine. Background: I've been riding MTB for a little over 10 years in the Southeast - lots of roots, short-steep climbs, loose conditions, and a fair amount of technical-twisty terrain. Also manage to ride the North GA mountains some with bigger climbs / descents.
My main ride is a full suspension cross country bike - dual suspension but with only 3" travel - and 26" wheels. 2 years back I built a Niner One9 single speed - super light, 29" wheels, racey geometry.
This season I'm back to riding my 26 almost exclusively. Why you might ask? Because the 29 has some geometry-imposed limitations that I find bothersome.
the 29" GOOD - it does roll better and handle bumps better. Seriously. My 29" hardtail feels about the same over roots, rocks, logs as my 26" with 3" travel. No exaggeration. It carries speed better through sand and over stutter bumps and roots. I REALLY like the way it smooths out a trail. Alao, as a big guy (6'1", 250lbs) it feels a little less like a clown bike.
the 29" BAD - because of the larger rear wheel diameter, almost all 29s ( mine included) end up with a chainstay length (the length from the center of the pedal crank to the rear axle) above 17 1/4" - this mean it is VERY hard to wheelie the bike, or to loft the front end, or to carry the front end level off small drops or logs. Over all the bike doesn't feel "playful" and you can't toss it around and body-english it through obstacles. It goes like a rocket as long as you want to be GLUED to the ground. I enjoy catching a little air and throwing the bike around, so this has become a deal breaker for me. I've also injured myself a couple times when the front end planted coming off an obstacle when I would have easily carried it on the 26" bike. Also, as a heavy rider, I can feel 29" wheels flex more than 26s, but that may be the individual wheels I've been on
There are a companies that are starting to radically rethink frame design to build 29ers with chainstays in the 16 1/2" range (Canfield, Kona, By:Stickel) so I'm hoping to test ride one. Maybe it will combine the trail-paving ride with some playfulness. Someday in a perfect world, I think my perfect bike would be a 29" hardtail that rides like a bmx bike, has a 1x10 drivetrain and weighs about 22 lbs. I'd park it next to my V8 Ariel Atom and my Duesenberg.
So, my recommendation? If most of your rides are really rolling hills, a 29" hardtail will suit you well unless you are small, then go 650B. If you are an ex-bmx er or generally like bunny hops, wheelies and riding like a 7 year old, stay with a 26 - maybe a short travel dual suspension bike. In either case, buy as light as you can afford, it makes a huge difference.