Ah, not exactly. First, a 29er mountain bike actually is running the same size 700c wheels as most road/cross bikes today. In fact, many of my buddies who run 29er mountain bikes run high end road racing wheels, no problem. So, don't get confused betweein 29 and 700, we are talking the same thing here.
Second, its not necessarily harder to ride a larger tire up a hill (that seems what rmwun54 is saying). If that were the case, we'd see all the guys in the TDF running 12" wheels like our kids run. Now, it is harder to overcome the starting resistance etc of a larger wheel, but once you have the wheel rolling, its faster and in fact, a larger wheel has a different angle of attack on offroad obstacles so it in fact rolls over obstacles like rocks, logs etc more easily than a traditional 26" wheeled mountain bike.
Don't believe me, go ride them if you can. I've ridden mountain bikes, 29ers and cross bikes, all off road. Trust me on this.
Now, given your desire to ride a dirt trail or tame singletrack, likely I'd get the cross bike. Otherwise, you'll have a bike that is slower on the road due to being heavier, larger rolling resistance with bigger tires etc. Now, if you end up getting into the offroad thing, riding more trails, riding in the mud a lot etc, I'd go with the moutain bike setup--as a 29er.
One option is to buy a Surly Karate Monkey frame--you could set it up as a mountain bike with suspension fork etc or set it up as a cross bike--it take 700c/29er wheels/tires just fine.
check out www.surlybikes.com