For one, certain ships should be equipped to handle re-entry, so that you can invade planets on the ground using those certain ships, IE Troop Transports, Frigates, Fighters, maybe some certain classes of Destroyer and Cruiser? Planets could then have ground bases, shipyards, supply depots, cities and such for you to destroy/combat. I imagine that you guys haven't planned on something like this as it would be a completely new combat setting, but I think it would be worth it. If you're having an Industry skill tree, buildings and such would be a great way to implement that.
In Atmo, ships would have to behave differently, air resistance, constantly firing altitude thrusters for larger ships, and probably the thing I want most: individual control over over fighters.
Just a thought, and if it's not something you want the project to go into, giving us a basic framework to work with over at the Modding community would be nice, so we're not starting from scratch.