Yeah, the game is littered with questionable at best gameplay choices and issues but i still like playing it. stealth in particular can be wonky as fuck, but i've got that ol' stealth game autism where i have to keep reloading until i manage to perfectly clear a section. thankfully the autosaves are like 5 minutes apart so i don't lose too much progress. also for the minigames there's an armor addon, printed circuitry or something that's supposed to make them easier. not sure if it gives you more time or what, but i always get it. look for it in the clearinghouse.
btw a tip - in some missions you'll be going up against npcs who are "good guys" like police, agents, etc and if you kill them you lose rep with your handler and possibly other penalties, though i'm not sure about that. so keep some tranq rounds around in your inventory.