My niggles...
The dog's dinner they have made of the Explorer interface compared to past versions of Windows, and the complete lack of configuration options re button size, button placement and text under buttons. Inexcusable. No 'up' button in Explorer. It should be there for those who want it. The menubars are disabled by default, a case of form over function.
The network activity icon; it both doesn't work properly (flashes seemingly randomly rather than in line with actual activity) and the colours for on/off are too close together. In previous versions of Windows it was very clear; in Vista they have messed it up.
The Start menu is crap compared to XP, and there is no option for an 'XP style' menu. Why not?? (You choose between '9x/2000' style, or Vista style.)
You can no longer shutdown with Windows key-U-U, or restart with Windows key-U-R. The shutdown button is now convoluted and involves a silly dropdown menu.
ctrl-alt-delete no longer brings up the Task Manager straight away, you have to go through an extra step to get to it, like in Windows 2000. I don't like this.
I could go on
