It's funny that something with no organization is still part of the model or even a model at all.
- Files are stored all over the place. Some applications spit out files to C:\. Some applications store configuration in the program files directory. Some store files in your local user (%appdata%) directory (where they should be!).
- Every application must use their own installer/uninstaller. This puts a lot of work into getting those right and making them clean up after themselves.
- Because applications store stuff all over the place (even in the registry!), it is difficult to know which files to backup or sync if you want your settings to remain constant on all your computers and recover them after a crash, etc.
I enjoyed having the responsibility, personally. I never thought of it as Microsoft's. I don't think anyone can stop what's happening though. Progress be damned! Koyaanisqatsi....
But with power comes responsibility. It's fine for them to do what they want, as long as they do it right, and that's why I say Metro is a step in the right direction.