The endgame is already frustrating enough as it is and the mutagen puzzle requires some thinking, or time to write down the mutagen combinations. I couldn't do it in one, two or even three trips to a safety hatch or the exit to the north. It was easier to just let the eye counter increment itself while I wrote everything down and then load my savegame before that.
I understand the change in tone and the peak in difficulty. I like it and I think the decision to make the character relatively weak again is very strong and adds to the atmosphere tremendously.
But why gimp and frustrate the player this way? I'm playing an RPG, not a frustration simulator. My character's tedium should not be mine.
At the very least make the counter stop during dialog so I can use the scanner and actually read what it says.
PS I know I can read the dialogue feed after the fact, but that thing refreshes with each transition and save, so that's not a reliable method.