1. Its most annoying feature in my opinion (and its activated by default) is that it caches all your most recently most programs into memory every time your computer starts. Not only do I think this is a stupid feature, it takes ages to complete, hordes the memory, makes your hdd go nuts, and most of all I had no idea wtf was happening with my new computer.
2. file-indexing is activated by default - Microsoft didn't seem to realize this in conjunction with feature #1 makes your computer go crazy every time you start Vista. And it took me a while to figure out what was going on. My new computer which i bought 2 month ago was thus brought to a crawl every time I started up.
3. Interface is pretty but not intuitive, a lot of stuff is moved around for no apparent reason, eg you now have to wade through 3 or 4 links just go get to your network connection properties, which is something that should be more readily accessible to the average user.
I know these are all options which can be modified, but hell it took me a good few hours to figure out, and it annoyed me like crazy. Windows XP in comparison just seems faster, simpler and gets the job done quicker.