I had a few ideas on how to balance carrier experience, while still making it be an impactful mechanic.
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Recruiting - Carriers receive 1% of experience (defeated ships) as bonus regenerating ships, used first in combat. This incentivizes playing aggressively with a few large carriers. Bonus ships would regenerate each tick, so they would be available for every battle. This mechanic favors the attacker.
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Salvaging - Carriers receive 1% of experience (defeated ships) as bonus ships, consumed once destroyed. This incentivizes switching from offense to defense with advanced carriers. This mechanic favors the defender.
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Generating - Carriers generate extra ships equal to 0.1% of defeated ships per tick. This is basically like industry at a carrier, so large carriers can potentially match small stars in production. This mechanic favors attacker and defender equally.
So those are my ideas. All of them use smooth scaling rather than progression points (such as levels every 100 ships) because that way they can scale more evenly throughout the game. A carrier that is strong early on but is kept safe will not scale as well as new carriers that are used on the front lines.
The actual values might have to be adjusted, but I think any of these ideas would be feasible to implement in Proteus.