I'm with you - I really like my 29er for AR! (Do I remember correctly that you also have an X-Cal?) At the moment Trek has lost my business due to the 27.5" thing, though it would be interesting to do more extensive testing because I didn't notice a whole lot of difference riding a 27.5" X-Cal for a day this summer. (Unlike a friend's 27.5", which is very different.)
My mountain bike is Trek's Cali (mid-model) with such crazy geometry that there is no room for a bottle cage (but I prefer a hydration pack anyways).
I thought there wouldn't be a difference, so was surprised that I (thought I) noticed it right away.
Totally unscientific testing though.....and I wanted to not find a difference....