There's nothing wrong with an alignment system, it just doesn't mesh well when you gamify it.
I dislike it because it doesn't map on to the way real humans think, act, and feel.
It doesn't need to, because it's in a fictional fantasy world. It's part of the game system, and just like any other part of the game's system you learn how it works and then play within that system.
Exactly.
Hit points don't make any sense either but people don't expect them to map onto real world experiences.
"No, no, I see why you're worried -- I've got this dagger stuck in my neck and I just lost two ribs to that last mace strike -- but I'm good for another few hours. Don't worry! A good night's sleep and I'll be a right as rain, you'll see, happens all the time."
Which makes some plot points kinda absurd but you just suspend disbelief. "Hey Aenevia? I know you broke your leg in the fall and that's why you can't join our party but we've found about 120 healing potions and this wand, maybe you could try one of those?"
For al the problems with the implementation of the alignment system -- and I agree it's flawed -- I'm happy to be playing a game where alignment matters. In BG3 I wonder if Lathander is ever going to get upset with my good priest for spending her nights with a chaotic evil undead thief.
Sure, you need "game systems" in a game. Hit points aren't particularly realistic, but they do allow you to play a game without a full (and probably overly complicated) simulation of the human body and its various reactions to trauma. I am fine with this because hit points generally get the messy details out of the way and let me play the game.
The problem with alignment is that it DOESN"T get the messy details out of the way. Rather, it forces the writers to pigeonhole every NPC into a daft framework that doesn't really have any payoff anywhere. Instead of debating character X's motivations at various plot points we are stuck with insipid arguments about whether or not they followed their alignment properly.
Better to scrap the whole thing and just write actual reactions that fit the situation and the characters that are being written. I am glad that 5e has done this.