Just a few ideas, I'm no modder/coder or anything but I always have a few ideas kicking around.
Randomised ship buffs:
Think starship legends, but upon finding a ship it has random affixes and prefixes like a diablo type rpg. Common, uncommon, rare, unique, etc. Even a reskin of the unique version of said ship type.
Battle map complexity:
Add more points of interest to the battle map. Black hole that sucks in weapon fire or even small ships. Could make the holes suck ships in one spot and toss them out another.
A king of the hill point, giving huge buffs to whomever controls it. This would take away from the big slow capitol ship abuse and allow for a less heavy handed way to shoehorn frigates in without being hugely bias in the skill system.
A flux point to overload or super charge weapons or shields?
Movable colonies:
Change the colony into a super capitol ship. Have a tool bar ability to toggle it into fleet and out of fleet. Doesn't even have to be a planet, could be a station. I remember an old tv show Shadow Raiders had moving planets like this.
Stationary defence:
The ability to build stationary defence in a system you've chosen to colonise. To help protect planets, stations, gateways, etc. Think mini stations that auto join battle of anything around them.
Anyways thats all I can think of for now lol.
