The basic idea of the game is to first shoot someone with a shotgun or some other high damage, low rate of fire weapon (left click), switch weapons (right click), then finish them off with whatever rapid fire weapon you have on you (left click again). This is mandatory; those that can do this will kill people in under half a second.
It's a bit frustrating, because most players don't think to do this making for very easy rounds. Maybe it should be added to the tutorial if it's going to remain such a fundamental tactics.
I love these types of games. As for controls, what another swarm-blob-thingy tactics game did was have an indestructible leader pixel that all other pixels under its command would follow. You already do something similar with the path drawing, but it's a pain trying to specify which parts of the blob you want to follow. Perhaps have the user hold down the shift key to select sections of the blob, with the ability to select multiple units at once by clicking and dragging. As for the issue with selecting the base itself, simply don't allow multiple blobs to occupy the same space - if they're too large to merge, then they should be diffusing across the map. If they run out of room to diffuse, then the base shouldn't produce any more troops until it does have room.
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