Is it just / ?
I kid. But really, besides “its all a file”, if you take away the gui, is the only difference the syntax ? How libraries interact? How disks are mounted ?
If we stripped all ms’s junk out and made windows open source, would we still prefer linux?
When you get to a very basic level, is one of them more efficiently coded?
Somewhat of a cheap answer, but I feel what illustrates the difference quite well is that Linux follows the design from UNIX, which was a research project with stupid amounts of money to at least try to get things right. On the other hand, Windows originated from an OS, which was referred to by its developers as “Quick and Dirty Operating System”.
And I do feel like these foundations have informed the design of all the layers built on top.