Not a direct comparison but I have a BPM 500w code 12 in 26 in wheel (30a KU123 controller) and a BPM CST 500w in a 700c/"29er" wheel (21a S12S controller) and while I haven't done any lab testing the 29er bike is heaps faster in total speed, on the same battery, my 700c setup builds up speed more slowly but goes faster, while the 26inch build takes off like a rocket like riding a bull (on lipo) but doesn't go that fast.
Its all technically comparing oranges with apples but I think going 29er over 26inch is a no brainer for geared motors if you got the option at least for riding where your mostly commuting.
In the last Olympics 2012 in Britain *EVERY* single rider that competed in the mountain bike event choose to ride a 29er over a 26inch bike.
*Edit* I decided to google that olympics "everyones" a 29er statement, I thought thats what I saw when I watched the event on TV but more accurately it was probably around 90% of them were 29ers. From the stats 9 of the top 10 riders were on 29ers as far as I could dig out of google roughly.