The list of potential problems with GNOME Shell I'm looking at (all in 3.4):
Visual hints: The user menu status is hard to recognize, as everything is monochrome, making it hard to know for users whether they are online or not.
Visual hints (2): You don't see whether you have new notifications (e.g. chats). I have installed a plugin to fix that, but it's not packaged for Debian AFAIK, which means extra work.
Chat integration: Having two ways to chat with people might be confusing to users.
Stability: I'm not sure how stable it is. I only have Debian's 3.4, and it's clearly less stable than GNOME 2 (or likely fallback mode). It crashes from time to time, probably about once per month. It also does not like resuming that much, and can crash, probably because it tries to render something before the Intel GPU's 3D driver is properly re-initialised.
But there are problems with fallback mode, too:
Flash performance: Flash performs much better in Shell than in fallback mode. In fallback mode, you will see lines on your screen as it draws a new frame.
Uglyness: Media applications look slightly ugly, as they are rendered with the dark theme, but metacity uses the normal theme.
In the end, I don't know what I'll choose for my users' systems. I personally am happy with GNOME Shell and don't want to miss it, but I don't know whether my users will be happy with it.