Player choice and The End.

[Cranky Old Man]

Simon is however a moron for thinking his being copied had any chance of taking him out of the body being copied from. This annoyed me to no end.

Why would he be a moron? It worked twice before.

I don't think you understand how this being copied thing works.
All this time, through the ENTIRE game, you've been playing the contents of the cortex chip found inside the worker robot at Omicron. Previous to the game, this cortex chip was loaded with a memory of Simon, attached to the body of Herber, and sent off in Simon's quest. It remembers what Simon in REED's body did previously, and even the life of original Simon, but the player wasn't actually there.
...but Herber Simon isn't able to tell the difference between a memory, and real life. It won't know until it's actually copied, who it actually is. Provided that Simon was smart, he was hoping for being a part of the memory aboard the ARK, just REMEMBERING what Herber Simon did, and not actually being Herber Simon itself.
There was a 50-50 chance of either alternative, but Herber Simon was blind to losing, both because it had worked so well before, and because he was really hoping to leave Pathos II for a promised land.

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I'm talking about the player choice to kill the WAU, clearly Simon-3's arm gets ripped off but shouldn't he also instantly die as a result since his protection suit that was supposed to withstand the high pressure just got torn apart?

Nope. You see, the instructions for putting on the suit states that you need a friend to help you actually SEAL the suit. (I think the button is situated in the back or something.) ...so the suit wasn't actually sealed, and the body got slowly pressurised in the airlock on its way out. That didn't stop you, because the gel probably compensated, protecting your bones, and so on. ...so I'm guessing that those cortex thingies can withstand abyss depths.