I don't like the idea of making a dozen different flavors of small ships with guns. "small vs. small" and "small vs. large" covers most of what an armed fighter is built for. How about some actual utility behind the fighter bay?
Drone squad: Similar to a certain scout craft's ability, these squadrons stick around a sector after you leave. They rapidly decay and can be attacked by interceptors, but will provide sector detail until they are gone.
Planetary assault craft: Armed with heavy precision payloads and atmospheric capability, these fighters attempt to wipe out a planet's infrastructure and population control up close. Kind of a rip off of siege ships, however they would be a fitting addition to a siege cap.
Mine squad: Not so much a squad as filing a cargo bay full of high yield mines. These mines fill the surrounding space and seek out enemy frigates or caps to home in on. Perhaps a heavy carrier would find this useful.
Movement hindering land mine: A Phase Jump inhibitor... land mine? Well, whatever helps you run away, I guess.
Repair drones: Not as precise as the nano cloud of the hoshinko, these large drones initiate field repairs beyond a ship's normal repair rate. Their large size makes them prime targets fighter intervention, however.
Defensive sensory drones: These drones scan the energy patterns of enemy gunfire and relay info back to the ship. These enable the ship to more quickly and efficiently attune its protective force fields, thus increasing its overall mitigation.
More missiles!: Just as its name suggests, the ship's cargo hold is modified into a makeshift missile bay, specialized against fighters, heavy ships, or planets. Designed with front loaded use in mind.
Extra Generator: The cargo space is modified to enhance the output of the ship's shielding, engines, or antimatter reserves.
Defensive Countermeasures: Designed to spoof enemy aim, guidance, or missile locks against friendly targets.
Communications buoy: A smaller, weaker version of the radio towers used to propel culture across space, modded to be launched from a hangar.
Mining ships: A small detachment of ships designed to assist frontier patrols with establishing resourcing and salvage operations. May gather from local asteroids or "scraps" from a field of battle. Clearly a Vasari favorite, but all starbases need something to pass the time.
Healing potions: Wait, what? This isn't Warcraft 3!
Artifact hold: Designed to hold minor ancient artifacts, trinkets of value, or enemy spoils of war(such as tech, intel, etc.) Clearly ripping off WC3 in mind.
and my favorite for last:
Tactical Assault pods: A team of suicidal shock troops/saboteurs/assassins infiltrate and cause all sorts of hell on the inside of large ships/orbital structures/planets.
Some of these ideas sound more like capital ship abilities rather than actual hangar options. The idea is that yes, some of the ideas are meant only as equipment options for a few specialized ships, rather than as a total fleet option. The ship would have to sacrifice fighter space to gain the extra utility. However, the idea is that they put more small things on the field, more things worth shooting and to be wary off. Of course, that means more screen clutter too.
