What I would like to have:

File recognition by content/magic numbers. Files are only recognized by extension right now and that kinda sucks.

A modern file system ( Liek fast and stable ), symlinks and beeing able to mount parts of the file system into specific folders.

A good editor that comes with the system.

A more stylish, simple GUI style. The current default style has far too much colors for me (And the "Classic" style is, well, old and square-ish) , and theres no good way to customize it without resorting to strange hacks. A good GUI should not be noticed IMO, it should just look and feel natural. The feel works pretty well for me, but I hate the look.

Oh, and beeing able to install software without having to reboot every other time would be nice.

What I actually like is the way program settings are (Supposed to be) stored (In the registry). Having all the config options in one place makes it easier to back them up (Or would make it easier if 1) programms actually did what they are supposed to do and stick all their config options into the registry and 2) Regedit didn't suck as much as it does). Beeing able to control what apps may add or delete keys from the registry would be nice (Like what Spybot can do, just built into the system).