A few of my personal pet peeves (note: every disgruntled user has their own, largely disjoint set):
1. The applet to inhibit screen sleeping went away. Without it, I often look up from working on a hard problem to discover that my screens have been blanked out.
2. Something GNOME-ish keeps grabbing my mouse, and won't let it go until I log in with SSH and start killall-ing anything with "gnome" in the process name. It happens once a day or so, I haven't been able to purposefully reproduce it, and it's really annoying.
3. The settings applet was neutered. It now looks like a cheap knockoff of MacOS's system settings, except somehow with even less functionality. It also seems like the GNOME developers simply forgot about it until about a month before the release, because many features that appear to be present are barely functional. For example, Appearance -> Theme only changes gtk3 themes, and most of the gtk2 themes don't have a gtk3 counterpart, so now about half of my apps don't look like the other half. Another example: the new settings applet stores network proxy settings somewhere weird now, so neither Firefox nor Chrome find my proxy settings any more.
4. About half of the GNOME configuration has moved to gconf to dconf, but there's no rhyme or reason as to which half. When I discovered the new settings applet, I tried to change stuff with gconf/dconf, except I have no idea how to figure out which applications use what settings storage backend.
5. A lot of applications don't have key bindings any more, or had them greatly reduced. GNOME 2 was pretty good about this, but many GNOME 3 applications are completely unusable without using the mouse.