I've not had much issues understanding what runs when, because for the most part I didn't need to care that much, and when I did it was possible to order/schedule systems in Bevy. That's even a bit easier nowadays too, since the API improved!

With regards to the chaos: I think it can be avoided, but like you said it requires a bit of discipline. I don't feel like it required that much more than normal software engineering (but I'm also the type of person that documents and tests everything even on personal projects lol). The plug-in system makes it easy to help bring order too.

This is all through a bevy-tinted lens, since I've done very little game dev (dabbled with UE and Godot) outside of bevy, though!

I agree with this - ECS lets you write totally decoupled, composable bits of game logic very easily, which is super powerful. But in my experience if you're not careful you end up with a hundred perfectly decoupled little things and it's really difficult to remember how they actually all come together to make the whole game you've built.

Easily grokable filenames and file structure are very important, and bevy specifically has a pretty nice plugin system which lets you really clearly 100% isolate groups of state/logic into more sensible sections instead of ultimately having some root level game loop that's directly setting up your 100 tiny little poorly named things.

Yeah, I'm one of Bevy's maintainers, and I've seen folks get tangled up (or overengineer things wildly) if they go in without a clear plan. ECS (and a strong compiler) makes things much easier to refactor, but I generally agree that the more flexible nature demands more discipline.