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?
Up until 95, Windows was mostly a desktop environment for DOS. From 95 to ME, Windows was an OS that used DOS as its bootloader and compatibility layer. Not sure how to put it, but it was simplistic and fundamentally different from Linux.
The thing with NT-based Windows (including modern editions) is that the underlying system is joined at the hip with the GUI. Whereas Linux with your choice of coreutils is a perfectly capable OS without the GUI, many features of Windows are only accessible through the GUI.
Given enough time and resources, pretty much anything exclusive to Windows could be ported to Linux and vice versa. A lot of the difference just comes down to history and the ensuing conventions, workflows, and file hierarchies.
Even if we stripped out all the cruft and spaghetti code from Windows, there would be lots of nasty idiosyncrasies in its design, informed by its OS/2 and VMS (see Dave Cutler) heritage, profit maximization, revolving door of devs and interns, and years of bending over backwards to accommodate legacy programs.