This is one of my biggest gripes stopping me from switching to Linux. I just can't give-up windows' partitions. I find Unix/Linux file system to be incompatible with how I like storing my files.
That's an old image, though - Windows has a C:\Users\youruser setup like /home/youruser for a while now.
I find the %APPDATA% thing way less convenient than ~/.config and I'm quite happy when programs have the "bug" that they still use ~/.config on Windows.
I like partitions to be at the root of my file system. And dedicate each one to a specific use. And even dedicate a separate hard drive for my personal files. When in need of transfer or repairs just move this drive to another PC and carry on the work while the former PC gets repaired or nuked.