Faction Mods:
Roider Union
Kadur Remnant
Legacy of Arkgneisis
Federation
Scy Nation
Underworld + Tahlan Shipworks (Cabal and Legio. Tahlan is where Legio comes from, btw)
Ship Packs:
Luddic Path Enhancement + Hegemony Expeditionary Fleet
Arma Armatura
Tahlan + Underworld (Though they add factions, I mostly got them for the pirate fleet variety)
Varya's Shipack (Slightly modified)
Other
Libs
Starship Legends
Trailer Moments
Speed Up
Combat Alarm Sounds + Combat Chatter
Console Commands + Captains Log
Better Colonies
Logistics Notifications
Unknown Skies
Rambling about my thought process with my list, other faction mods, and what not:
I'll ramble about my whole list because I think seeing the sum of it's gives my list context, will be helpful for understanding what informed my choices.
Factions? Not many. My list is small-ish. I tend to rotate them in and out. Bigger lists kind of get too chaotic for me and I'm not a fan of the load times, so I keep it small. Kadur, Arkgneisis, and Roider Union fit right in and feel more like additional pirates/subfactions rather than full fledged factions. Those three I usually keep in. Then I'll have one or two more I plug in on rotation to check them out. Scy Nation is very lore friendly, but I don't always interact with them so they aren't always in. Federation was too nostalgic for me not to grab.
Legio and Cabal are mostly incidental because the main attraction with those mods are the ship packs. That said, the cabal makes hyperspace travel and smuggling more risky which I highly appreciate.
I also try to keep things lore-friendly-ish. So I avoid anime, meme mods, and mods that push the tech in crazy directions. Though, admittedly, I'm kind of a hypocrite because a lot of the time rule of cool gets the better of me XD I couldn't say no to the FTL inspired mod and the mech mods are hard to pass up. Also of note- Rather I'm playing with or without Nex also changes the way I look at adding factions. With Nex, the chaos of more factions is fun so I might plug in a couple more than usual. With a tighter more vanilla++ list I want less.
Tiandong is going on there as soon as it updates. If I ever get around to doing a League playthrough I'll give Mayasuran Navy a go. Diable I like to throw in when I'm doing Nexerelin. Xhan Empire is on my radar, but I haven't tried it yet. HMI looks a little out there, but I do like the junker aesthetic so I'll probably try it at least once at some point.
Tahlan and Underworld do so much to enhance pirates that they are a must have.
Varya's I adore and love most of the ships in it but I did go in the faction configs and got rid of a few. Stock standard it adds way too much frigate bloat. It dilutes early pirate battles into just picking on and blocking up a few near defenseless Spades and hounds. So, I got rid of the Spades, one of the Hound variants, the pirate Battlegroup ships, the Direwolf, the Henchmen, and few other things I thought were redundant or silly. The end result was immediately better, between Varya's more interesting frigates and underworld the early pirates weren't push overs anymore.
Ship/Weapons I'll probably add but disable a few things too (like that giant Ludd ship) Missing Ships I haven't tried but would need to disable the capital ships, patrol boats, and probably look at dropping Expedition Fleet and figure out what ships overlap between it and the Luddic Enhancement pack. I have enough ships and that would require some testing so I haven't got around to it. If I shake things up I'd probably shelf my other ship mods for a bit to see what I like better. As it is, I'm already thinking of pruning things back a little.