For Sins 2, the whole planetary system needs to be looked at. I want to see planets become more interesting in general, not just in terms of defense, but in development, too. A seperate tech tree of planetary development would be a good place to start. It could include habitation, defense, even political techs to research. And while they're at it, add some sort of ground war invasion option, too. It's such a big list of possible changes that it needs another major overhaul, as with Diplomacy. Hence, I doubt it will apprear until a full expansion or sequel is announced.
As for planetary defense missiles, Sword of the Stars has them. Basically, a planet fires a handful of harrassing missiles evey so many seconds. It doesn't really accomplish much except to possibly destroy an already weakened vessel. If that is all that is to be added, it really wouldn't add much to the game except to chase off some very weak planetary assaults (really, an orbital defense platform accomplishes the same thing).