Humans in Starbound are probably the weakest storywise. (Novakids don't count as they have zero story intentionally.)
Feels both just general bad story and conflict with the Protectorate stuff they added relatively recently. It really doesn't make too much sense that Earth is home to both a human military force and a (human-led?) galactic federation-type thing. At first it was pretty simple:
Earth was where everyone lived, but the USCM (I think that's the right name) put military bases and prisons offworld for some reason. They had standing orders to shoot intruders when they lost contact with Earth, and that's about it. It was awful then and it's even worse now. Why are both they and I slaughtering the last remnants of our species?
And this isn't even that compelling storywise either! Why is everyone on one planet? Why hasn't Humanity expanded? What possible gameplay reason is there for this?
Hell, Starbound's story is just straight-out awful. It's all laid out at the beginning, there's no actual satisfying conclusion or feeling of change, and more. I want to save Earth! It just feels like an intergalactic tour rather than an actual compelling story.
Honestly, I'd be happy if the devs just made various themed expansion packs for Starbound. Not like bits of DLC or paid updates, but like tons of actual content relating to a theme. Like ships with FTL style combat and stations. Or more advanced and immersive colonies with stuff like puke mentioned. I'd definitely pay for that kind of thing. Not that it'd be better free, though.