What if, an additional research option, gave more of a chance for your weapons systems to come back online after a direct attack?
I would have it so you could never have a 100% recovery, however perhaps max would be around 80% after many many upgrades.
Right now, if I wanted to attack a planet that had a moderate amount of defense, I would bombard them with enough ships as to minimize my losses. However, from then on I would need less and less ships to do the same job, and if this player was an enemy I could keep his planet compromised. This is fair, but for game mechanics it tones down the challenge for us, and stifles the abilities of newer/dedicated players who are trying to swim in a pond of big fish. Perhaps instead of buying this upgrade with resources, it could be time based. Age of your empire, or perhaps purchasable with Rubbies? Giving your planets or ships a permanent boost, would not only be very attractive, but it would give new players willing to invest into being great, a chance at just that. You could make it account based, so that even if the "server is reset" you still get to keep what ever bonus you purchased.
Also to combat people dumping everything in only defense, you could keep it so that the missiles launched still permanently destroy them.
This will do two things. It will cause players to become more spread out as to avoid, or hunt players. It will change the point Liam Jay said a while back about the unnecessary need/use for Missiles. He is right. Why buy 20 missiles when you can build one RIP to do the same thing, only with the RIP you get to keep it and it has an unlimited range?
Just a thought. I don't think this will vastly change the game, however it might add a different approach to combat, and colonizational placement.