Simon is definitely ‘out of his depth’, and while the player is generally smarter than he is there are a couple ways I rationalized his reactions. Spoilers below contain all major plot points and I strongly recommend anyone reading this play the game.
spoiler
Simon repeatedly demonstrates he has no idea how he ‘came to be’ on PATHOS-II; he doesn’t understand the mechanisms involved in his arrival.
When/if the player discovers the recordings in Catherine’s lab, it’s up to the player to realize that Simon 1.0 lived on after his brain scan; If my memory serves correctly Simon does not comment on the events that happen after his scan. Just that there’s a recording of him.
Even all the transcripts about ‘continuity’ showed that the real people in PATHOS-II had trouble understanding the process; the person who sits in the chair is never the one that carries over. Admittedly this is the core debate of the story; people who look at it mechanically vs people who believe in a higher consciousness. I’m a mechanical guy.
In regards to his emotional outbursts on the lift; All of WAU’s creations seem to have problem regulating emotion. Speculated to be due to physical limitations of the hardware they’re trapped in. Even though Simon is the most stable, it’s still reasonable to think that there are either logical processing limitations due to his “flat scan”, or processing limitations of the cortex chip when presented with something as complicated as a human intelligence.
Even if we’re going to presume he is as Catherine described; “a sound mind in a sound body”, this could just be his breaking point. The underwater facility. WAU’s creations. The physical trauma of the train crash. The terror of being hunted by the psychotic helper robots. Maybe that’s just his limit.
That’s all in defense of Simon 3.0’s reaction about the events surrounding the powersuit.
I have no defense for his reaction at the end. From a narrative experience it makes sense that we wouldn’t immediately wake up on the ark; but he’s been through this before. Limitations aside, he’s got no excuse.
Though, this actually leads me to a side-theory about Catherine’s ultimate fate; that she seemed ‘uniquely suited’ to being trapped in an omnitool because of her lack of strong emotion - but what if she recognized the limitations of her environment? The one time she becomes truely emotional is when the omnitool dies.
Those who have suffered and decided that others must suffer too because “they turned out OK” or to “toughen them up” were broken by their suffering and that’s just deeply sad.