I have read other people wanting more and more super-duper ships, but I feel current system is already pretty good. That said, It would be nice to have a ship of excep[tional firepower. I will call that the Admiral ship.
Like in star wars, there are star destroyers and the super star destroyer.
It would be impossible to just buy this ship. You would have to upgrade a capital ship up to level 10, then move this ship to a gravity well where you have a capital ship factory. You would then upgrade that ship to be the epitome of mobile firepower in your empire.
There would be only 1 of those allowed in-game. It would likely take 2 or more capital ship slots.
This behemoth should not be as powerful as a starbase. It would reset the ship level back to 1, to reflect that many of the systems were ripped on the hull upgrade to be replaced by better ones. At this base level it would be much more powerful than a plain capital ship at level 1.
It could have 2 custom upgrade slots, like the starbase, but all upgrades would be combat-oriented, like: upgraded offensive systems (weapons/antimatter/cooldown), enhanced defense systems (shields/hull/regeneration), upgraded engines (better speed/maneuverability/faster jumps), fleet support (enhances fleet attacks), carrier bays (fighters/bombers) and maybe an all-rounder upgrade (modestly upgrades all systems). 6 upgrade options and only 2 slots... choices, choices.
The Admiral ship would retain the characteristics of the original capital ship: a carrier will still be a carrier etc.
That would make it interesting way to have a super capital ship, for me.