Nexerelin adds a lot, so it might not be for you yet, but it makes Starsector more like a 4x game, with invasions, diplomacy, spies(agents), and some other stuff.Spoiler
Nexerelin forum page - https://fractalsoftworks.com/forum/index.php?topic=9175.0
On the faction side a good introduction mod is Scalartech Solutions.
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Scalartech Solutions forum page - https://fractalsoftworks.com/forum/index.php?topic=18845.0
They are a fast high-tech faction, with some good weapons, and fitting their ships isn't too complicated.
For a expansion of vanilla ships, Ship and Weapon pack has lot's of good vanilla-adjacent ships, but similar to Nexerelin it is a lot for newer players. Another good mod would be Torchships and Deadly Armaments, which is full of nice balanced ships.
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Ship and Weapon pack forum page - https://fractalsoftworks.com/forum/index.php?topic=11018.0 Torchships and Deadly Armaments forum page - https://fractalsoftworks.com/forum/index.php?topic=17856.0
For most mods, you'll need to also download and activate these libraries, or the other mods won't work:
GraphicsLib:
https://fractalsoftworks.com/forum/index.php?topic=10982.0
(Also for this one, you might want to change the settings of the mod, because this adds all kind of graphics and lighting and stuff. Here's a link to my guide for that https://fractalsoftworks.com/forum/index.php?topic=19597.0)
LazyLib:
https://fractalsoftworks.com/forum/index.php?topic=5444.0
MagicLib:
https://fractalsoftworks.com/forum/index.php?topic=13718.0
Finally, for stupid, unbalanced, but really fun, there's Kingdom of Terra. This faction whacks, smacks, and pushes other ships, instead of just using weapons. If that isn't enough, there is a ship that is a giant T Rex skull, that chomps ships.
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Have fun with this one - https://fractalsoftworks.com/forum/index.php?topic=16902.0