Hmm, I think I should make myself more clear:
Why should we have roundabout systems for 'punishing' the use of warheads or other resources by shortening the next wave timing, increasing AI progress, etc., when it could be distilled into what it ultimately is: a wave of ships attacking your planets?
Let's say you use a warhead, and the AI doesn't like it. Why bother with incrementing the wave timer when you could just have it generate a new wave on a short timer, or construct a nasty structure that requires proactive action? In that case you'll either have to defend as you normally would, or you'd have to attack to prevent further nastiness. I think that'd be a pretty interesting way to do it.