The Ark was pretty much "We're all screwed anyway, might as well finish what we started", as well as the vain hope they could get some kind heaven on the Ark instead of hanging out in the hell that is Pathos 2. Even simon is initially skeptical and eventually decides "Well, it's not like I have anywhere else to go or anything else to do", it's mostly Cathrine pushing him that gets him to come around. What it might do is preserve a few human minds for a couple thousand years, which if not great, it certainly the best the last of humanity could hope for at that point(unless the surface isn't as uninhabitable as it looked from space).
That's what I figured. It's why I went along with it at first. But then we learned more about the Wau, and it seems so odd that the story's gives it such awful treatment. The Wau and it's potential is never brought up by any character, it's diminished and ignored by quite a few - It's hardly afforded any resolution, much less a resolution befitting one of the most fascinating and philosophical points in the game.
WAU, on the other hand, has a lot of potential, but isn't really able to create anything useful. Like Catherine says, it's like Cancer, albeit with some kind of bizarre intelligence. However, all of it's attempts to preserve humans resulted in zombies, robots that think they're human(despite all evidence to the contrary) and Simon(who is basically a wired up corpse in a diving suit held together by structure gel). Despite simon being the most sucessful so far, it's questionable how viable he would have been long term. Very little that appears "sentient", not the mention a lot of the ones left alive sure as hell didn't look like they weren't enjoying being kept alive(The one woman who was wired up and kept alive through an artificial set of lungs(outside of her body) sure as hell didn't look happy).
By what definition of sentient? By what definition of human? By ours? Does our definition matter anymore, given that humanity's wiped out and won't be coming back? We never see anything from the perspective of the Wau's minions, and yes, trying to murder us the whole game is kind of a dick move. (Although given the Proxy in Theta shoves you into the Wau's growths, which give you the hallucinations to begin, it seems like it's trying to preserve people) But on the other hand - can we really call them zombies, just because we don't understand them, their motivations, any possible sentience or intelligence they might have? "Being human" isn't an arbitrary gold standard of existence now,
it certainly wouldn't be in a theoretical future where humanity's gone.
And besides, the Wau's improving. It's only been off the rails for a few months, and in that time it's progressed from from just shoving people into robot bodies without reason, to making things like Simon and Catherine. After all, Simon is one of the latest to be created, and one of the most human as well. Given time, the Wau could improve further. It could find a perfect solution, where they retain their humanity and are viable long-term. It could bring back all the scans it has, and maybe even figure out to replicate new ones. As for the people in the structure gel - we never really speak to them. We only speak to Anne, who doesn't seem to have been complete consumed yet (Or, for whatever reason, the Wau refuses to completely consume despite taking in healthy individuals in Theta. Maybe the gel's different there because of what Akers did.) All those others we find trapped in it? They're probably happily hallucinating of a perfect world, just as Simon was for the brief moments he was in there.
And just... why not let the Wau inherit the Earth? What's there to lose? Anything worth preserving's gone. But with the Wau, there's a chance of getting it all back - or at least, creating something of equal value, if you can accept the idea that inhuman does not mean invalid.
It's such a fascinating question, and the game completely wastes the chance to ask it.