Theoretically, the larger 700c wheel will be more efficient because it spins slower and the tire probably has a lower rolling resistance. However, in practice there is no real difference. It is true that you will need to use a larger gear on the mountain bike in order to go the same speed as the road bike, but you will be putting in a similar effort. Personally, I find that stock mountain bike gearing is a little too low for me for road touring.
Crank length is an issue, but think of it more as a part of the gearing; a longer crank will effectively lower the gear. Play around with Sheldon Brown's gearing calculator (www.sheldonbrown.com
), especially the gain ratio part, in order to convince yourself of this.