> Green button made the window grow but not fully maximize - I never understood the point of that

It’s supposed to grow to the size it needs to fit the content. That button was never a “maximise” but a “zoom” (you can confirm this by checking the “Window” menu in an app).

> Red appears to quit, but actually doesn’t, it merely closes the window, which is confusing for the simple case of only having one window.

It depends. The general rule is that for apps which can only ever have one window (e.g. System Settings), closing the window quits the app. For apps with multiple windows, closing the window only closes the window.

> And the analogy of traffic lights doesn’t really work.

We (the users) are the ones who call them traffic lights, though. As far as I’m aware, Apple hasn’t suggested that as an analogy.

> though, nowadays it goes fullscreen, which is great

The old behaviour is still there, if you ⌥+click.

> The classic one that everyone talks about is the weird way apps are installed by dragging an app into a folder

The insight there is that (most) apps aren’t really “installed”. You can grab that file (actually it’s a folder, a package bundle) and put it and run it from anywhere.

> Also, that UI wouldn’t always show up, I believe because the app itself has to be coded to trigger it.

Unless I’m misunderstanding you, that UI is part of the DMG. If an app is distributed as a zip, for example, you won’t see it.

> but I think it’s overlooked just because “that’s how it’s always been”.

But it’s not. You yourself listed an example where it changed (zoom/maximise). Installing apps with PKG files used to be more common. The scroll direction thing isn’t that old, it was only some time after iPhones that trackpads changed the default motion.