Really being much more into road bikes than mountain bikes, I find it a little surprising that the pedal clearance above the ground would be changed when building a frame for a different wheel size. Is this because these things are being envisioned as riding through sections of deeper mud, so that greater ground clearance is needed? Or for bunny-hopping over bigger logs in the trail? I'm sure there must be a reason for the decision, but it isn't too obvious to me what is considered sufficiently important to make raising the center of gravity of the bike/rider combination an OK compromise. Do you know what reasons are given?
I'm sure the frame geometry is affected when the wheel size increases and I don't think the pedals are higher off the ground to meet any special riding need. When I first got the bike, I felt like I was WAY higher than before but it really isn't that bad. The bottom of my pedal stroke is both about 1.5" farther from the ground than on the 26er. As a percentage of my foot's distance from the ground, that's not insignificant, which I guess is why I notice it. It's a non-issue most of the time but if I hit a slippery root, it feels like I slam to the ground faster and with less opportunity to save myself than in the past. But that may just be inexperience.
I would say you have very good experience slamming yourself to the ground! ;-)
Ha! To be fair to the new bike, I've hardly fallen off it at all but when I have, it's felt swift and a bit surprising.