- It's UGLY. It takes a lot of code, time and experience to write any kind of good GUI.
- They all look different because there is no standardized way of doing things.
Because of these points I can only picture an ugly GUI that everyone copied and made a de facto standard, because it was some geniuses idea of "perfect". The standard look really has no artistic value to me and I get bored of looking at the same thing, no matter how functional it is. I rather expect software to stay consistent from version to version. If instead every application was laid out the same way, that would be silly. Yeah, so in example, winAMP can be as different as it wants from windows and it still makes sense. But move information or features around constantly (firefox), and I'll need a cigarette to get over it, and get used to the "new" thing.

- 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.
It's funny that something with no organization is still part of the model or even a model at all.

Portable installation has mitigated these problems on the windows platform, as you've probably figured out. (I'm talking about programs being compressed and being usable after decompression, instead of needing tons of regkeys just to work.) I don't remember when this started showing up, but that was one development I liked in the world. In my opinion, it can be a better choice than your typical desktop installations and upgrades. Of course, with corporate software, you use what they put out and there are reasons behind that.

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.
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....