Granted this one would require a bit of work, and would probably NEVER see the light of day BUT:

It would be nice to have different ways for us to interact with other bases and base battles.

examples:

people have different styles of play, I favor hacking / spy play over raw pvp. For people like me it would be cool if you could use your base to hack into other people's bases and, lets say reduce the efficiency of 1 attack or defense module to 50%, or reduce the shields by 25% for an hour, something like that.

Other people really like invading planets. Where's my Deathstar? I'd like to blow up someone's planet with a base!!!