The most [1] annoying difference to me is the Alt/Cmd vs Win/Alt key swaps. In this case, Mac has precedence, and Microsoft decided they would place their new Windows key to the left of Alt.

Also, 10 whippings for whomever at Apple decided to put the Fn/Globe key to the bottom left of laptop keyboards, and move Ctrl over. It's the first thing I swap on a Mac (used to use Karabiner, until macOS finally, years later, decided to implement the setting), and I always trip when using a colleague's laptop. These kids don't respect no traditions!

.. that rant over, I must recognize that Ctrl isn't used as much in GUI apps which prefer Cmd, and only us relatively few terminal junkies care.

[1] second most, perhaps, after swapping Delete & Backspace.