Champions Online has introduced a lot of Devices that turn your character into a "monster" with its own special abilities.
That's not exactly what I have in mind, but I could see them creating ships with less customizable Bridge Officer slos and instead with pre-determined skills, some of them unique.
These ships might have only 3 Lt.Level BO slots, but come with additional 6-7 innate powers that represent their unique capabilities.
I would also not mind a special new tier of ships that is not higher or lower than existing ones - simply a tier of ships with less bridge officer abilities all together that can play in their own "league", so to speak. Imagine a ship with no more than 6 Bridge Officer Powers.
They could create both types of ships by re-using the existing ship classes (plus introducing new ones).
I could see a "Restricted Play" league that would give all ships 6 Bridge Officer Abilities at every tier of play, but just different weapons, consoles, hit points and shield values. The result would be a system where ships of different tiers are closer in power and it would be possible to have Tier 2 ships fighting side by side with Tier 5 ships without anyone insta-gibbing ships 3 tiers below them.
Ships could be assigned point values and so you could assemble teams of the same point value with different numbers of players and different ships.