Recent developments in technology are making certain things about 29"ers that were negatives less so, or eliminating the problem all together. These are a few of the technological applications that I think need to become widespread in the 29"er world.
Through axle hubs: With Rock Shox's excellent Maxle and now, the Maxle light, there isn't any reason to not have 20mm through axle front hubs and put them on all front suspended 29"ers. The effects of having a rock solid connection between the fork legs and wheel are immediately felt and make a 29"ers front end more predictable and fun to ride. I would even suggest that many rigid fork options have 20mm through axles. Especially lightweight carbon ones.
Full suspension bikes could really benefit with the addition of a through axle on the rear of the bike. In fact, Salsa Cycles is currently working on through axle rear drop outs for it's upcoming Big Mama full suspension 29"er. That should tell you something right there.
Tubeless Ready Tires: There is no question that 29"ers benefit from ditching the archaic tube and going sans bladder. To do this though, you have to either "buy into" a current system such as Stan's, Bontrager's Tubeless Ready System, or Mavic/Hutchinson's set up. You could go to the "ghetto" tubeless set ups, but sometimes certain tires are not so friendly, shall we say?
Anyway, my suggestion is to have all future tire introductions be of the tubeless ready type. Why not? If your tires, (as Continental's already are) are rated for use with sealant, have a tight tolerance, consistent bead that is strong, why wouldn't you do this? The tires could be used with tubes or run tubeless. A "win-win" for tire manufacturers and riders alike. This should be done ASAP.
Along with this, rim manufacturers should also be doing things to get their products ready for tubeless use. Bead locks, consistent, tight tolerances, and specific rim strips could go along way in making products more attractive to riders who are obviously looking for solutions to tubeless set ups.
Tapered Steer Tube Technology: My take on the front ends of 29"ers is that they could stand to be stiffer and stronger. A great solution to this problem is the tapered steer tube. The 1 1/2" to 1 1/8" taper on the steer tube provides more strength with a minimal weight gain, and with upper end forks and headsets, it could be the same weight as a traditional head set in 1 1/8th inch size. The bigger diameter on the bottom of the head tube means a bigger weld interface for down tubes and allows for larger diameter down tubes in the first place. Both would make the front ends of 29"ers stiffer, stronger, and steer more precisely.
Those are a few things I think should be widely implemented into new 29"er models. All three would enhance the performance and lessen the negatives of any 29"er.