Maybe a hull mod to convert a flight deck into a drydock, to repair frigates at a very slow rate...
That'd be an idea.
Though "a" flight deck would be too generous, because there are a lot of quite small ships that have "a" flight deck.
For one it'd be very difficult to balance if small carriers (destroyer/cruiser size) had access to that.
More importantly, though, it makes no sense to repair&refit a frigate in a Flight Deck that it cannot physically fit into.
In addition there's a little visual problem: Some modded ships (like the alien Behemoth or the Omega for example) - and maybe some future vanilla ships - have multiple flight decks, but they are not right next to each other (as they are in the Astral's large Flight Deck), but are small seperate bays instead that a frigate could not physically fit into.
In the end I think it'd be a better solution to modify how flight decks on a ship are handled and displayed.
Instead of representing Flight Decks as an arbitrary number, where it shows 3 in both the Astral's and the Omega's case even though one is a large one and one is three small ones, they should be named as they are.
(For those who do not know the modded ship I'm comparing the astral to:
http://fractalsoftworks.com/forum/index.php?topic=2058.0
http://img337.imageshack.us/img337/7646/omegaf.png)Before:
Astral - 3 Flight Decks
Omega - 3 Flight Decks
Not possible to tell a difference until you see their sprites.
After:
Astral - 1 large Flight Deck - able to service three fighters at once
Can equip Hull mod: "Allows any large Flight Decks to repair&refit Frigates
(at a much much slower rate than fighters) in addition to (or instead of) Fighters."
Omega - 3 small Flight Decks - able to service three fighters at once
Not able to equip aforementioned Hull mod.
Now, deciding whether or not it should be a hull mod or a native feature of anything with a large Flight Deck is another, more balance-related, issue that I doubt we could settle right now.
The main thing, however, is that ships who have larger or smaller Flight Decks visible in their sprites should have their stats represent that instead of just having an arbitrary number assigned to them - one large bay that fits 3 fighters is not the same as 3 small bays that fit 1 each.