It sounds like you simply have too many units, and I don't think you'll be able to just add more units in a game like SC2. Showing the units graphically, as well as complex computations like pathfinding take a lot of computer resources. One option would be to find a different game which supports larger armies.
An alternative option would be to do some sort of work around such as "banking" units. By this I mean you would have some sort of numeric representation of your units, but not actually have them on the field. Say you have 1000 zerglings, but only 100 are actually on the field. When one zergling on the field dies, a zergling is automatically spawned, and you deduct 1 from the bank.