Thargoids have not always been fair game. At some point during their introduction phase, when it wasn't possible to take any of them down, and even later on, it's been speculated a lot about possible thargoid factions. Now, apparently, all of this has been washed away since those theories don't have any ground, at least in terms of game mecanisms. It could have been an interesting twist, having some "friendlier" thargoids, not actual ally, but curious about us and ready to "trade" some knowledge and items (about the guardians maybe, giving rise to joint investigations here and there).
I could imagine a puzzle game about deciphering communications with them to understand some basic intentions. But I guess such an idea was not worth the investment and it was easier to just use the dogfight system already in place, and simply make the thargoids just a variation of the PVE experience. I feel what we need is an evolution of the core gameplay, with new interactions and new activities, that would go past shooting and scanning, before we can imagine the introduction of a sentient alien race with which we could have friendlier interactions.
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About the possibility of other sentient species with interstellar travel capacity without us being aware of it already, at first I felt it wouldn't be plausible and I guess simply because I get to see the whole galaxy in our galaxy map and thus have the illusion of basically knowing pretty much anything of interest there is to know (which in a way seems to be the case in the current state of the game).
But we have to remember that less than 1% of that galaxy has been actually visited yet. So there very well could be another sentient race just starting to expand, more or less advanced, not necessarily curious in the same way as we are, nor in need of expansion as us, driven by other needs and feelings, that we haven't yet encountered. They may be stuck in their own bubble because of their overall philosophy and/or biologicial constraints. Maybe they can only survive in the proximity of brown dwarves and they're surrounded by their worst fear : F, G, K, and neutron stars. ^^
3 sentient races within a 400 billions stars universe which 99% of them haven't yet been visited? I'm pretty sure it would still count as "very rare", like the lore states.
That other specie could or could not have advanced interstellar travel capabilities. It could reside in one fully colonized system, and have very crude colonies in neighboring systems with no direction communication (and we could be the ones helping them restoring a link... and clumsily creating conflicts in their societies)
They could be more or less as advanced as the 22nd century human civilization, and yet still have valuable things to trade, because their technology and knowledge would be of a different nature than human evolution. So I definitely wouldn't dismiss the possibility, nor would I reject the idea was it introduced in the game in a proper way.
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The only real question to me is: what kind of gameplay are we talking of with the possibiliy of friendly alien species?