I am fairly sure most people would agree that one of the biggest mysteries and most intriguing secrets in the game is The Severance. I hope there will be a quest about uncovering the reasons behind The Severance, attempting to reestablish communications with Earth, and trying to repair the quantum gate. Additionally, it would be a nice bonus if there were also something about trying to establish communications with Atlantica.
This is mostly to quench our curiosity. It doesn't necessarily need to lead to significant gameplay changes. Maybe just implications of how this big reveal/events may change things in the future. A quest like this would also serve as closure/conclusion to the game and may be the "ending" the game needs.
P.S.: To be honest, even if the quantum gate has been shut down, making travel back and forth impossible with our slow spaceships, Alpha Centauri is only a pissing distance away from us on a cosmological scale, being just 4 light-years away. Since radio waves travel at the speed of light, it should be possible to reestablish communication after 4 years (8 years for back-and-forth conversation) if Earth is still there. Unless higher-ups in Raana have decided to keep these reestablished communications a secret for some reason...