god i know i'm gonna get flak for this, but i'm going to reference moo3 for a sec (yes i know, different game, sucky game, all that, but put that aside for a sec). I like the idea of planetary bombardment, ALOT. Having that option attached to military ships, and not transports that is. Scaling the amount of damage done with the sophistication and number of weapons involved in the attack (plus any modifiers like mass drivers).
Thus in the early game, you could have say, a fleet of 4 fighters, well armed, that would do very little, but some damage to both population and structures. And in order to completely eradicate a planet's population, and improvements, such a fleet would have to bomb the planet over and over, perhaps too many times to be practical.
Now in the later game, with better weapons and bigger fleets, more damage would be done. Say a fleet of 5 cruisers could do, 10 or 20 times the damage described in the first scenario. Thus takening only a few turns, or perhaps even 1, to kill off a planet's population and trash the imrovements.
That is, at least i think, something simple and worth implementing. I really hope the SD guys peek at this thread, cause it's something i think a lot of people would really love to see in the game. Obviously there are all sorts of other options you could add, dropping a percentage of your payload, 25%, 50%, to do less damage, or a blockade similation with planets surrendering. But i think that's beyond the point, something simple, like i outlined above, would really satisfy alot of people, at least in my humble little opinion.