Weren't the crew already doomed before WAU

[Abion47]

The problem is that none of the WAU's creations are suitable for long-term survival. Every single "survivor" is either comatose, a robot, or a walking corpse. The comatose people can't help for obvious reasons, and the robots are all either in denial or insane, so they can't help either. The people who are walking corpses aren't going to last long, since their entire existence depends on the structure gel, which in turn depends on electricity to stay active. And that's assuming that the corpses themselves don't start degrading.

Another thing is that assuming the WAU is sentient, and assuming the WAU is well-meaning, any chance of cooperating with it is unlikely, since there aren't any reliable ways to communicate with it. The WAU was meant to be a warden unit, not a full AI, and as such there aren't exactly HAL-style terminals on the walls to talk to it. The only people able to effectively communicate with the WAU are the people who consumed so much structure gel that they themselves are going insane.

And even if they could communicate with the WAU, that's working under the lofty assumption that the WAU is something that they can see eye to eye with. On TVTropes, it's called Blue and Orange Morality, where a being is not Good or Evil by any conventional means, but whose priorities and moral compass are so dissimilar to our own that it reaches conclusions that we couldn't understand. The WAU is not being malicious, of course. It is merely doing its job by any means necessary, and from its eyes it must figure that it is doing good. But it cannot understand what it means to be human, which means that things like intelligence, coherence, individuality, autonomy, and general comforts of living are not something that it deems important - as long as people can be considered "alive", then it has accomplished its task. And to take it even further, it will have succeeded under its own terms if those alive people are also kept under a state in which they can't possibly jeopardize their safety or the safety of others. Humans cannot reason with such a being, because even what seems "logical" won't necessarily be the same for us as it is for the WAU. We just think too differently.

I don't buy that the WAU intentionally created Simon. There is nothing to suggest that the WAU cared about anything other than keeping people "alive", using the loosest possible definition of the term. Every being it created was either alive but inert, stark-raving mad, or hostile to the point of being completely feral. Even Ross wasn't really all there, to be honest. But even if Simon was created by the WAU for a purpose, Simon's body isn't a permanent thing. Like I said, Simon's body depends entirely on the constant flow of electricity from the battery pack as well as the continued integrity of the corpse he is using as his vessel. Once either of those things fail, Simon is dead.

As far as other underwater stations, that isn't just a theory, that is canon. A map (I believe it was in Upsilon) shows seven other stations spread across the globe:

Spoiler below!

The purpose of these stations isn't known, but an important thing to note is that the map shows Alpha, not Pathos II. This isn't a map of general underwater installations, it's a map of Carthage points of interest. Perhaps it marks other underwater bases where Carthage is conducting other experiments or stuff.

So yeah, there is a ton of potential for sequels in this universe. I just greatly disagree that there is one in which everyone gets together with the WAU and becomes best buds.