So first of all I feel like I would remove SOME of the insta-death scenarios, I felt like they were a bit overused throughout the game. Insta-death can make things feel tense, but when used in the wrong way, can make things annoying/tedious for the player. This change would improve the overall game imo.
Secondly, make guns more accurate by default and REMOVE auto-aim and upgrades. I have no clue what they were thinking with the aiming system. This would encourage skill over a silly mechanic like upgrades and auto-aim.
SPOILER for the last change.
Would love to hear all of your ideas!