Bandu's got the idea.
You don't even need to have all ships boardable to make fleet ships interdependent. For instance, just have different cap ship types give different bonuses to their team.
If the medical frigate is alive, infantrymen, presumably boarding enemy ships, get slowly recharging health in the field to symbolize having medical facilities for the fleet.
If the communications ship is alive, the commander has the ability to see everything on the map - enemy ships and allied alike.
If the fleet carrier is alive, the team gets more ship respawns or more bombers, or more advanced fighters spawning once in a while.
If there is a freighter alive in the fleet, fightercraft spawn with larger payloads.
I think that, although sometimes unrealistic, game mechanics like this for space maps would add a great element of depth and give the same battle a different outcome and strategy each game.
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