In terms of QOL mods:
Combat Chatter (as mentioned above) - has both flavor and practical use
Combat Alarm Sounds - again, both flavor and good practical use
Leading Pip - shows a designator to help you lead targets, though obviously doesn't account for evasive maneuvers
SpeedUp - what it says on the tin
Logistics Notifications - what it says on the tin
Hostile Intercept - notifications (and autopause option) for when a fleet targets you
Automated Commands
Captain's Log
Lightshow - beams colored by effect for more consistent threat profile
Content mods:
Nexerelin, of course
Commissioned Crews - integrates with a bunch of faction mods and gives both some flavor and sometimes helps with weaker factions
Blackrock Drive Yards - I think it's only an interim patch right now, but great style aesthetically and mechanically
Shadowyards - as above
Diable Avionics - Nicely balanced and neat assets
Anything from Vayra, Vayra's Sector and Ship Pack in particular
Starship Legends
Seeker - instead of adding factions, puts a lot of esoterica and unique bits and pieces in the world
Xhan Empire
HMI suite - not overpowered, and add a fair bit of extra content beyond the faction(s) themselves
Secrets of the Frontier
Arma Armatura - it's mechs so a different feel, but mechanically incredibly well done and includes other fighter goodies as part of the package
Tahlan shipworks
Industrial Evolution
Underworld
Torch Ships
Audio Plus
Unknown Skies
There are plenty of other quality ones, those are just the ones I'd more or less auto-include on any run. (and there are lots others that are probably very good that I just haven't tried!)
By and large mod-ships and mod-factions are pretty decently balanced, though there are some outliers. Most notably in my opinion, Dassault-Mikoyan is popular, high quality and includes good 'beyond faction' content, but I still think it's overtuned.