It's not the filesystem's fault, the question here is how you use it. Most of the customs of *nix users in regards to usage of storage could be recreated in NTFS running Windows, and much of what happens in Windows with files and folders can also be done with ext* and company with a Linux kernel under the hood; it's all a matter of how programmers decide to make their programs act. I bet that if you just do a raw port, just converting calls etc to the corresponding, several Windows programs will install in a linux system creating a "Program Files" folder and it's own subfolder inside that, and if the port is done correctly, it will run from there; i got lots of programs on my Windows machine that originally came from Linux that fill my userprofile root folder ( %UserProfile% aka %HOMEPATH%) with dot-prefixed folders instead of using %AppData%, though they pollute the folder tree with misguided entries, they run just fine.