Let's see, off the top of my head...
- Mailman doesn't work. And of course everybody wanted that one.
- I can't remove domains without fiddling around because the default install thinks Tomcat has been installed and removed It never has been installed by my choice since the RS license doesn't support Tomcat.
- Previous protected directories are no longer protected. Have to re-protect them all again.
- If you're running any additional scripts against your access_log or error_log you need to reconfigure them because they're moved.
- File Manager doesn't allow you to delete files unless you debug it.
- Frontpage Extensions has been reported as broken for some, doesn't affect me since I detest FP with a passion.
There are a few others, but it's late and my memory is bad to begin with.

They're all discussed on the Plesk forums. Just don't look in the Bugs thread, because it's perpetually empty for some odd reason.
That's not to say I don't like ver 6.x, because I do. Just that this has been
the buggiest Plesk version they've ever released. It'll all get sorted out eventually I'm sure.