More offset on suspension forks. Even if 38mm is ideal for 26" bikes, the 39mm of the extended 29" fork is just not proportional, and restricts frame designers. Notice how most all rigid 26" forks even run greater offset, typically 43-45mm? 29" wheels, to keep the same handling quickness (trail), require extra offset over 26". Now the larger sized 29"ers get steeper head tube angles to gain back some quickness, but on smaller sizes that would cause toe overlap (toe hitting fron tire). 29" wheels, all else being the same, eat up 31.5mm worth of toe clearance, and smaller bikes don't have that to spare. Over-compensating offset, going like 45mm for 29" forks, would help designers create even better handling smaller sized 29"ers. Already for "medium" bikes this is very much an issue. Often top tubes have to be longer, and handling to be slower than designers would have preferred.
Hub spacing. The 100mm front spacing dates from ancient road bikes. Now we're building hardcore MTB's with the same spacing, and lots of room of that is eaten up by a disc mount lately. Making for flexier wheels. Rear spacing. For decades road bikes have 130mm. MTB's got 135mm. Again, lots taken up by the disc mount, and cassette bodies haven't exactly gotten narrower over time. Rather wider, going from 7 to 8spd around '90 or so.
Upping hub spacing front and rear by some 15/20mm seems more than in order, especially for 29" wheels which have the same rim diameter as road bikes, making spokes have little angle on the nipple to work with.
Weird offsetting on rims may help a little bit, but that's not a solution.
Someone mentioned it with respect to Bontrager, not sure what that was about. Tire-rim standards. Tires seem wide, rims seem undersized. Tires are hard to keep on the rims most of the time. What's up with the 700c standard, why do most tire/rim combo's fit loose enough to throw a tire on a rim from across the room rather than with a bit of help from the tire levers?