An even Darker SOMA [ending spoilers]

[Cranky Old Man]

But the WAU doesn't think, it just does. It doesn't follow any plans (I think). Having to create a puppet, making it hallucinate, controlling it in order to claim the ARK and launch it doesn't fit the WAU's way of being.

I think you've missed how to unlock Johan Ross's office at Tau.

WAU stands for "the WArden Unit". It has protocols to safeguard either the inhabitant of Pathos II, or the entire human race. It's more of a synapse culture than a program, so it's so advanced that you can't actually order it around. You can only watch it grow. Watching it grow was the task of psychoanalyst Johan Ross. He noted that post impact WAU began evolving dramatically, into something else. He had no idea why, and he was supposed to be an expert. He was fearing that WAU would become self-aware, and that's why he set out to stop it (with a "virus" of essentially formatted gel). WAU keeps people alive because that's "its plans". That's its protocol. If launching the ARK with WAU inside it also would count as "preserving the human race", then WAU will do that. If the only means by which to launch the ARK, is by building a dead body into a robot and loading a template brain scan into it, then WAU will do that. If it has to manipulate this robot through social interactions with other brain scans, when it will do that. To the WAU, you're just a tool through which it enacts its protocol. You're not even human.

Besides, if you were the puppet of the WAU, why would the monsters want to stop you?

That's a good question. Maybe it's because these are indendently operating entities have been severed from the WAU, and doesn't recognize you as acting in its best interest? I mean why would they try to cause ANY robot harm? You're not trying to harm the WAU - at least not until Johan Ross begins directing you.
...or maybe they're acting as a set of easy obstacles to overcome in order to create a fake challenge to overcome, to keep you thinking you're winning? If you fail, then WAU can always create another robot and put it back in the pilot seat in the beginning. Most monsters just hit you hard anyway. Don't you find it strange that they won't kill you?
...and another point: Why does the WAU heal you? As Catherine points out, those flowers are interfaces with the WAU. Every time you put your hand inside it, it sends nanobots into your blood stream to repair damage. ...so it's not working against you. You are its agent.

Relating to Catherine's cortex chip. I guess that could be a possibility, but wouldn't that also include Simon's body aswell?

Yes, I guess it would, but it would create a better EFFECT to turn Catherine into the monster at the end. ...and then maybe show that the satellite has begun to form WAU growths, maybe?