My only exposure to motion control was a bid on a centrifuge system used to mix blood specimens. The thing had to go from still to really fast rpm's in what I considered to be almost an instant and then stop on a dime. The software wouldn't have been too tough but the motor and mechanics of the bid were beyond our reach.
Just wondering what sort of mechanisms that you're attempting to control? I always figure the hardware for such things is much more involved than the software. But then again, you can get a lot of hardware off the shelf these days that's just waiting to be put to some unique use.