"If the opposing players most potent armor and/or 88 flak gun units are eliminated in just that one action phase, the rest of the round will be of little matter, unless the scenario has been structured so that time is more important than enemy units destroyed."
But why would you put your only potent asset in a position to be eliminated in the first round of the game? Either poor gaming, or weak scenario design.
"If the enemys main firepower component is removed early, its simply mop up time after that."
I agree - that is how you most often win the game. Any number of situations can bring that about, including luck, design and poor play.
Your idear of a tiered kind of Move&Fire makes some sense. Though perhaps the reduction ought to be a bit more severe than -1, -2 or -3. The problem with shooting on the move is not realy penetration, but acutaly hitting anything.