I have a BD Fly Team Ti 29 that i got for a screamin deal and couldnt pass it up...I used to mtb a lot when I live in Oregon but recently wanted to get back into it...my old mongoose zero g is still in the garage and puttin around...
I have only a handful of significant trail rides with the 29er...first, I could roll over bigger objects than i thought...I am still getting back my nerve to ride the technical stuff...and some of this stuff I have ridden is pretty technical FOR ME....visually, due to lack of saddle time, the big tires seem like they would be harder to manuever...each time I have gone, I have been able to ride what I previously had to walk through... I think this based on ME and not the ability of the bike.... If you are just rolling on more cross country type trails, I would not hesitate to say get a BD 29er... I used to use clip in pedals/shoes , but for the technicality of hte stuff I was riding I switched to a 5-10 shoe and 10 pin flat pedal so i can get my foot off faster so I dont take a header (although it didnt help last time out!)....

If you plan on riding super technical stuff, I dont know really what to tell you...so far my bike has out performed me while riding...no troubles with the bigger wheels...if smaller wheels make you think you will have better control, they most likely will since you will have faith in their performance

just my $.02