Warning: contains arbitrary opinion, selfish demands and random flamage.
1. the "stretch icon" item on the context menu. WTF is this even for?
2. "notes" in the properties dialog. As you can't see these or search on them directly, they strike me as pretty much useless. If I want to make notes about a file, I put them in the filename.
3. emblems. Anyone actually use these?
4. "empty wastebasket", unless you are actually in the wastebasket.
5. The "start here" icon. Or the "computer" icon. I don't mind either of these, but I get the impression they haven't really been thought through. What is the "computer" meant to represent? Why "start here" when I never do?
6. The "overflowing" wastebasket - unless you are literally running out of space on disk. Don't make my desktop look untidy unless it is!
And some positive suggestions:
I really like the fact that the Windows property dialog shows properties appropriate to the thing represented - for example, clicking "properties" for the Network Neighborhood icon gives you network properties. That would be nice to have in Gnome too - e.g. "computer" properties would tell you about your computer.
I want a quick search bar in the file browser. Just to search the current folder and show only matching items. But maybe it would integrate with the beagle search stuff.
Anyway, I like Gnome and I think it is pretty usable.