Only problem I had with the MTB on the trainer was spinning out the tallest gear as anotherbrian mentioned above. With the Kurt Kinetic I just put it in the largest combo and spun 95RPM, still a great workout.
As far as riding position, I never thought too much about it. I can't get as low obviously on the MTB but I mounted bar ends (remember those? :-p), mounted parallel to the ground, to vary my hand positions and get out front.