The Windows 3.x UI was always ugly and didn't make any sense ;) But that's the 90's, I'm talking about the 80's.

For instance: AmigaOS 1.3 (notice in the bottom-most screenshot how the buttons don't have '3D edges':

http://toastytech.com/guis/amiga1.html

'3D' UI elements were introduced later in AmigaOS2.0, and I remember how the user interface style guide made a big fuzz about how UI elements that appear raised are supposed to be clickable while flat or recessed elements shall be used for non-interactive or disabled UI elements which cannot be interacted with.

Actually this site is a pretty awesome collection of operating system UIs. BeOS still looks nice, almost like retro-modern pixel-art.