There aren't that many mods with campaign-layer mechanics due to how hard these are to code - you're playing as THI, they have Survey Fleets and Mercenary Fleets with custom fleet AI which is hard to make work right.
Legacy of Arkgneisis adds a quest that ends with you finding a ship that has to be restored for its full potential, that mod also adds a bunch of heavily d-modded ships as derelicts for you to find. They aren't extremely strong, mostly a novelty factor.
Hazard Mining Incorporated doesn't add any quests, but instead adds multiple handmade systems, each with their own little quirk or enemy for you to fight - both in inhabited systems and systems out there in outer parts of the sector.
Roider Union has ship refit mechanics similar to Tiandong's, but they refit civilian ships into combat ships instead.
Gates Awakened adds a short questline to obtain access to few Gates in the sector for fast travel.
Tahlan Shipworks adds a bunch of ships that are found only as derelicts when exploring, most are RNG if recoverable, but also tend to be quite powerful, so it more or less evens out.
