Why would you limit the amount though? There should be an unlimited amount, but perhaps make a LOT of deterrents from being able to get more. Perhaps the credits, metal, and crystal needed could doubled for each one, along with an increase in fleet capacity (twice, then four times, etc.), and fleet supply (twice as well, then four times, etc.).
Keep in mind that there can be multiple flagships, perhaps one for one fleet and another for another fleet.
I think it could also just be a super-beefed-up capital ship (a sixth class).
Think Star Wars, the Empire had multiple flagships for different fleets.
- PR-0927