The funniest thing for me, though, is the implicit assumption we should have direct say over how it goes down. Yes, I realise this is a game, but why should we get a fully authoritative say? Sure; drive some of the direction, within boundaries? But the notion we have some sort of inalienable right to dictate how it all goes down? lol. no.
I'm all for engaging mechanics and player agency where we can help form long term trends, that change the game to some degree; but there's a point where too much control leads to a point where frontier is listening to a select few. That never, ever, ends well.
Frontier have been hinting 'the big bad' since the game's inception; it's there in actual game history. They are returning. It's not us returning, it's them. They. Who appear to be, at least to begin with, at quite the advantage. And they're ambivalent of us at best. I take no joy nor would I want the entire bubble overrun, this isn't going to work as a game mechanic.
But decent chunks of the bubble? Thargoids shifting presence about as they continue to look for whatever it is they are looking for? Absolutely. We all, all bought this game knowing that some threat will/ does exist. You can essentially mitigate most all of it, including other players, but it's fundamentally broken thinking to assume we should be able to mitigate/ obviate everything.
If you believe there is a story being told, then we have our part to play. And we just don't know what that is yet, or to what extent. But if a war is coming? If the other race just doesn't want to sit around the campfire and sing songs and be super friendly nice guys? That should have far reaching impact. We should all know we're not alone. It's going to be a very very difficult balance to hit; but for this game to have life left, things have to change. A static, stale universe, is an atrophied and dying one.
tl;dr - portions of the bubble imho should end up being rumbled by the big bad, and others not, so that the non-combatants and their support, can move resources, defend or explore, with reasonable expectation of continuation of freedom, and yet have the reminder, they are not always alone.