Units should be told to go somewhere, and you could assign waypoints. Then, when one unit is walking/driving/flying/sailing off, in gorgeous animation, you order another unit somewhere else, and in this way several units can move around simultaneously. This would look great on a large map and if the animations are anything like those on the Civ3 Site, the graphics alone could sell the game.

And for missiles, you would choose Launch, and then choose its target, whether its a city, unit, or blank tile. The Target cursor would be green withing the missiles range, and red outside. Once you launch, the missile will fly, continuously and smoothly, to its target, flying over other units and taking the shortest possible route (over the poles, perhaps?). If a SAM site tile improvement or mobile sam or SDI was in its path, it would shoot at the missile while it was still flying, almost RTS style...