Quote Originally Posted by victory View Post
It's not a big mess. You generally got one .file or .directory per program that carries the program's name. That's all stuff you would need to store somewhere anyway, and it's in an usable arrangement. The only difference between checking out app data with ls -la in your home directory, or looking inside the OS X Library folder, is that in the latter case your hand-managed data directories are not listed.
Not at all the same thing. The OS X and Linux way separates the app binaries and "built-in" data from user-unique data including config. The latter is stuff you might want to manipulate or back up. The apps themselves might be gigabytes in size, and are not unique (you can always re-download or install from disc, and might never want to install that version again because there is a newer one) so you generally don't want to bundle them with your unique data.
And you usually get one folder in Program Files per program. Also, one folder in AppData per program.

Beyond that, you are just arguing for specific software mentalities that are independent of the OS platform (which seems to happen a lot with advocates for Linux). Mentalities that are (mostly) being followed now, even on Windows. The big problem was that there wasn't a single unified location to start with, and lots of developers don't want to "break compatibility" by changing their patterns.