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But the WAU is clearly self aware, as it blew up the heads of the scientists, when it knew it was in danger. Which begs the question of why it didn't try and stop Simon once he had the special goo.
I suspect it comes down to plot holes. Maybe with computer game projects the writing gets less attention or resources than it would in the film industry (or not #Prometheus). So there are plenty of minor plot holes or inconsistancies.
'One thing I see standing in the way of this idea is that the WAU has been able to control life and manipulate matter, energy, to the point where I don't see why it couldn't adapt to the new environment on a decimated Earth and basically take it over.' - the surface of the Earth is basically dead, along with all life on it, so I think the only place the WAU could take over is whatever sea life is left alive. Which is already seems to have done to a lot of species.
Personally I didn't see much point in killing the WAU, as all the damage had already been done, and at least it was keeping the station functioning and various forms of 'life' alive, for better or worse.
Simon doesn't have blackbox, plus Ross is aiding him.
There is another theory it's not WAU that made simon. WAU doesn't control its creation so who move Imogen Reed's body, assembly it with cortext chip and put simon's brain scan on it at upsilon? This is still a mystery, perhaps a sequel or prequel are planned.
There is a long discussion about this in soma subreddit: https://www.reddit.com/r/soma/comments/58my25/spoilers_i_didnt_wau/ (see the top comment)
I forget who spoke about this, but it was probably Akers, who said that the WAU would indeed convert all life on Earth, essentially destroying it.
edit: j0j0, that reddit was a great read! thanks for the link!
Apparently, in an earlier version of SOMA this "robot" and Simon had the same "nature" (i.e. a walking diving suit full of structure gel) and they woke up at the same time in the first room. You can find remaining of their dialogs in the game's sounds folders. Later in the game's developpment (after Transmission mini-serie) Frictional choose to give Simon an other nature giving him the body of Imogen Reed. The blood you can find in the first room (where Simon wakes up) suggest that the "other robot" (the one you find "dead" in the room where you can find the omnitool) brings Imogen Reed's corpse by ventilation shafts, cuts her head and put at the top the robot's cortex ship (from the UH near the pilot seat)... perhaps following a strong impulse from the WAU (maybe the WAU was trying to bring back power at Upsilon: if you think about it the majority of the robots - Catherine, Carl Semken, Robin Bass - is awaken when Simon restart the power, and there was little power remaining in the station - only 13 days - before that, which also could explain the importance of the Currie and its reactors for the WAU). :)
The Omnicron genocide didn't happen, because it was self-aware. Or maybe in a little extent. Self-preservation was programmed into it and when it feeled threatened, it overcharged the black boxes. For the WAU, it was a little cost to kill everyone, it could reanimate them anyway. The WAU's program sort of realized that if it dies, it can't preserve humans.
So, the WAU is more of a simple AI with programming errors, not really an aware individual.