There are so many tactical options and things to consider here that they're not really countable. I've found that strict combat caps on skill levels help a lot too. The real game-breaker here is if you have caps, you have to cap skill levels, too, because on paper, they add directly to damage. (Which makes them too versatile for the point cost, in my opinion) My players, fortunately, are not combat rules optimizers, or my game would be ruined.
It all boils down to this:
Make them prone, use skill levels to add damage, knock them out. I really don't like this, as it's insanely un-superheroic and un-fun. I think that if you take the add to damage off skill levels in superheroic games, the problem will more than likely solve itself.