there needs to be a system for concrete ship production, and then ways to earmark ships for yourself from that supply, as well as demand (ask)? them to build you a certain ship they are capable of constructing, for lots of money and/or reputation.
"cleaning" out markets doesn't make any sense, and is only there because of systems that are entirely undeveloped. ships shouldn't be randomly generated. it's too random and makes no sense.
This. It just adds un-fun grind to the game.
I think it makes sense to limit faction military market access to reputation unlocks only and have commissions either the "top tier" requirement as Megas has suggested before, or a separate thing all together that just mitigates ship losses slightly when fighting that factions enemies.
But as far as what's available on those markets?... if it doesn't work this way already only those ships and weapons the faction actually uses (more technically: only those weapon ids contained in the variant files linked to fleet generation through the faction file) should be available on the military markets for that faction. The black market can have a very small, VERY overpriced, randomness beyond that. I am talking like one or two rare random ships or weapons per market. Think the scene in Aladdin where the street hawker runs after you yelling like "wait, wait I have something extra special!"
The rest of the black market should be discounted general weapons (tier 0) that pirates typically use, D-class ships, cheaper supplies and fuel and finally an assortment of, again VERY overpriced, military market ships and weapons that would normally be locked behind that factions rep, besides the top tier stuff of course.
Imo, seeing random weapons and ships outside the faction in their markets just really breaks the game world's immersion. I always cringe a little seeing the Phase Lance on Jangala when I start a new game because I just don't see the Hegemony really selling one. If anything, they would destroy it if they didn't use it themselves because they wouldn't want to see it on a TriTachyon vessel later on after selling it to some independent trader.
**edit** Yeah not the best example I know, remembering that Heg eagles actually use Phase Lances... but you get the idea
With so many new markets and worlds opening up with the Cartography post, I think this kind of market generation is pretty supportable too without locking the player out from too much. It also makes exploring new factions' markets more enticing and rewarding.