Perhaps instituted as a sort of flagship system, as opposed to capital ship system. Flagship being, of course, the lead vessel of a fleet or even an entire navy. A flagship of this type can be spawned on at X cost or perhaps with X health debuff or what-have-you.
Like the flagship of any fleet?
I really like the Nomad idea. Having an incentive to have a hangar bay with a bunch of spare shuttles, like some of the more RP small ships I've seen, with a single power block, a couple of thrusters, and a storage maybe, with a really cool passenger interior. For everything noncombat. Maybe you have some lightly defended corvettes, with pd turrets to protect from assassination missile, and a shield or two, to protect from some scrapes and scratches.
Anyway. Enough RPG hopefulness. At least there should be some comparison weight or block limits on flagships. Like, as a fleet of little cargo vessels less than 500 blocks, I only need a ship around that size, but if I'm leading a frigate defense fleet, I need more than a dinky hunk of junk to command(and respawn off of). It wouldn't make sense that the flagship HAS to be bigger, but it should be on the same class(ok ok, ship size). Although I could add a bunch of different limits, which wouldn't be too hard to program I'll do it here*.
Although it draws this post dangerously off topic, the idea of respawn on ships is fundamentally tied with fleets and the ability to almost have spares, and in-the-field respawning and reusing. No matter if it's a faction member running out and acting as your fighter support, or if it's a Nomad respawning on their iron snowflake after not noticing the pirate station.
*To keep it less cluttered and stuff. Lets make some bullet points.
1. It needs to be either the largest ship or 80% of the mass/volume of the largest ship.
2. It should have a minimum size based on numbers. Your frigate can lead a fleet of 15 frigates, but one drone the same model or smaller then it's 99 other fleet-members.
3. Respawning should have a flat out min size. If through a need for power or simply a minimum ship size, a simple fighter squadron shouldn't allow a practical zerg rush. A frigate or a medical corvette, however, probably could.