Here’s an idea I have been thinking about for a wile: Super sized ships.
A Class of ship that upgrades like both a cap ship and a star base, meaning that it would both gain levels and you could research and then buy upgrades for it. The number of upgrades would be determined by the amount of hard points it has. Every time it leveled up, the size of the ship and number of hard points would increase, but not instantly, you would have to take your ship to a upgrade facility upon level up , say a super dreadnaught dry dock (which is where you would build one), to upgrade the ship size and number of hard points. Each level would let you build an additional 4 hard points. Also everything built on to it would be more effective with each level. It would start out about twice the size of a cap ship, but by level 10, it would be huge, and able to go toe to toe with a star base and eat it for breakfast, lunch and dinner.
The ship would have abilities that would not need hard points like a regular cap ship (such as crew effectiveness abilities) and also some that would (like repair bays or something that extends its shield over other ships). But mostly you would build more weapon banks, large armor plates, shield projectors, more fighter bays, specialty weapons, and so on, customizing both the utility and the look of the ship. You could also remove a upgrade, if something you built isn’t working out for your style of play, and build something else onto that hard point. Each upgrade added to the hard points would have a different visible look to it. It would truly be a unique ship, and you can only build one at any given time. When you build it, it would become your flagship. It would be very expensive to build and upgrade, and would become the cornerstone to your assault force.