The 29in front wheel allegedly gives riders the “roll over anything" feeling up front, but the smaller 26in rear wheel apparently offers snappier acceleration.
Here's the single speed prototype from 2006.
This year, trek has added a geared hardtail and a full suspension version.
I understand the theory behind the 29er, but I am a little baffled by the 69er. Wouldn't the "snappier acceleration" of the 26" wheel be hampered by the resistance of the bigger wheel in front? And with the smaller wheel in back you'd lose the 29" advantage of "rolling over" obstacles. Other problem: you'd have to carry 2 different sizes of tubes with you, although if you're running tubeless, that wouldn't matter.
I haven't really looked into getting a 29er, first because I love my current bike and second because I didn't think I would gain an advantage, at 5'8" and 155 pds. It seems to me that taller and/or heavier riders would gain more benefit from the bigger wheels.
Interesting idea, kudos to Trek.