Stand over height is so low, not a consideration on either bikes.
For reference, Both my 26 and 29 are M size HT's. My 26 is 8.2kg and my 29 is 8kg. The wheels on my 29 are way more expensive but lighter than my 26 wheels. But there's still more rotational weight in the 29 wheels. But I got the 29 for marathon and ultra distance racing where acceleration is not important. I live in the Pyrenees mountains and most of my riding around, acceleration is not needed. Momentum is more important for a flowing ride and efficient style that can go for hours.
The 29 wheels have the advantage of grip, esp. climbing. I can now climb loose gravel out the saddle when the 26 wheel would spin and threaten to throw you over the front kind of thing.
Wheelbase is longer. I whack my crank arms more on rocks on the 29. Either the bike is more planted, I run more sag on forks or the longer wheel base is spanning the obstacles that rise up to kiss my crank arms?
Flickability is the biggest difference for me. The 26 is so much easier to get off ground or transplant. 26 is quicker to respond. If I make an error it is easier to recover. I love it that when 26 goes off a good line into rough rocks with pot holes, I can recover it by jumping and skimming over the hazard - usually
For me, I kept my 26 with intention to train on it but it's now collecting dust... the 29 is fun but in a different way.
