For mods that are vanilla-adjacent, I would recommend: Interstellar Imperium, Underworld, Ship/Weapon Pack, Outer Rim Alliance, Secrets of the Frontier, and Scalartech Solutions. (Some of these do require some minor tinkering to get them to run on the most recent version of Starsector, but it shouldn't be much more than update the required version and check the end of their threads to see if anyone's done a repackaged jar or anything.)
I will also recommend The Knights of Ludd; it has player-acquirable boss-ships that are very much not vanilla-grade, but it's got some very interesting takes on actually-vanilla-balanced low-tech ships, and is just generally really well done.
It's also possible to run Nexerelin in pseudo-vanilla mode, turning off AI faction conquests & colonization fleets; this is actually what I tend to do, as I like its improved start features & Prism Freeport & remnant-related mission chain.
And, last but certainly not least, I'll also recommend RATS (Random Assortment of Things), which is probably the farthest of these off of vanilla balance, but also really neat.