I think the game should bring in "hero ships" as a core mechanic. We already have a few cases that are almost there; the Offspring ships, and the various "quest reward" ships, and even science ships.
A "Hero ship" becomes a ship that a leader can pilot. In this model, a "hero ship" with a leader can lead a fleet, instead of the leader leading the fleet. (This simplifies how Offspring Ships work as a bonus)
Hero Ships have distinct designs than the ships-of-the-line; they can have different sections and even ship types. Each slot can be locked to a specific component, have a default component but allow customization, or be fully free to be customized.
If a Hero Ship has a default component in a slot, you can always use that component even if you lack the technology for it, and ditto for locked slots; a psionic avatar might have every utility slot locked to psionic shields, or whatever.
You can build Hero ships of each ship size - so a Hero Corvette, a Hero Frigate, a Hero Destroyer, a Hero Cruiser and a Hero Battleship. These may (or may not) have extra features compared to the base ship (like how Offspring versions of the ships have upgrades over the baseline). You'll be limited somehow in how many Hero ships you can have.
The ship designer will have a separate tab for Hero ships, which includes quest reward ships. The quest reward ships currently act as if every slot was "locked"; the game designers can choose to set slots to "default" or "unlocked" so we can retrofit those quest reward ship with upgraded components and keep using them in the end game!
The commander of a fleet will be piloting a hero ship. We can add features to the leaders that impact their hero ship individually, and even permit non-admirals to lead fleets. This means we can have "hot shot pilot" military leaders whose main boost is to their ship, compared to ones that boost the fleet more. Naturally Hero Ships will have an extremely good chance to retreat if their ship is damaged while the fleet hasn't been defeated.
In short, I want to find a submerged cruiser, and upgrade it and have it with me until the end game, piloted by AHAB.