It seems to me, that the difference between shields and armor, is that armor can get holes in it
With an energy shield, it should be easy for the protection to remain balanced in each direction until the entire field collapses.
If shields were to be left almost normal, and the armor were altered as discussed below, you could get a nice divergence between large and small ships. (Set the balance so that shield and armor are equally effective on a Cruiser, say. Then small ships would be better with armor, and bigger ships better with shields)
It would also create a mid-game situation where large ships are available, but they are only useful for non-combat jobs (since shields haven't been researched to worthwhile levels yet.