I have an idea for the later story of Subnautica 2.
I think it would be amazing if, after spending most of the game believing the original colony failed and finding blackboxes from colonists who died, the player eventually discovered a small group of colonists who actually survived. Maybe they could be located very far from the starting area, possibly somewhere closer to the World Tree in a biome that hasn’t been added yet.
Instead of surviving through constant reprinting, perhaps this group embraced the Angel Combs and adapted themselves to Proteus. Over the years, they could have built a small functioning settlement and learned how to eat the local food, tolerate the environment, and live permanently on the planet. I think it would make for a really emotional reveal. You would spend so much of the game thinking everyone was gone, only to eventually hear another human voice or enter a habitat and realize people are actually living there.
It could also fit the multiplayer story really well. The four playable characters could be investigators who were reprinted decades later, while this surviving colony represents another path humanity took, instead of changing the planet to suit humans, they changed themselves to survive on Proteus. The ending could then involve the possibility that Proteus really can become a home for humanity, even though it originally seemed completely uninhabitable.
I think keeping the surviving group relatively small would also preserve the lonely feeling that makes Subnautica special, while making the discovery of living people feel incredibly significant.