1) The overview is _painful_ to use on larger screen. Application menus have a tighter pointer locality, and when done right (which no, GNOME 2's were not at all right, they were horrible) involved less contextual overhead and wrist strain. Keyboard accessibility is great, but it can be more inconvenient to switch between mouse and keyboard than to just use the mouse, especially when using primarily mouse-driven applications.
2) The workspace management removees the utility of workspaces. Workspaces were a killer feature of the Linux desktop. GNOME 3 makes them incosistent, hard to access on multi-monitor displays (fixed somewhat in newer versions, but still not as good as an always-visible switcher), and really just trained me stop noticing that Windows 7 lacks them entirely.
3) The hot-corner is obnoxious. It's also very obnoxious in Windows 7. However, Windows makes it both possible and super-easy to disable. Right-click the hot-corner, uncheck the menu item, done. People who use mice on unstable surfaces or who have slightly less than perfect motor control frequently hit those ****ing annoying hot-corners by accident on a frequent basis, completely disrupting their work flow. Clicks represent actions. Pointer movement means a change of possible targets, or it means your wrist brushed a track pad, or it means the table was bumped, or it means that the laptop surface shifted and the mouse slid. Mixing click-for-action and point-to-target is a good way to tell a lot of people "you can't use this OS, go away."
4) The new focus on full-screen everything by default. I don't even full-screen most apps on a 20" monitor. You can't imagine how little I want a full-screen window on a 30" monitor. Really. Full-screen makes sense on phones, tablets, and even netbooks. It does not make sense on a giant multi-monitor workstation.
5) No on-screen window/task management by default. Yes, the old GNOME 2 window list was lame. OS X did it a bit better. Windows 7 did it way better. GNOME 3 forgot that task management is something that workstation users need to do (including both quick launching of applications or monitoring running ones). The overview is nice sometimes, but not all the time.
6) Various little details. The lack of Power Off in the system menu is a common one. Yes, yes, tablets and phones are never powered off because they are not PC hardware. The giant $2,500 PC in my bedroom with the glowing LEDs and fans that could power a small plane really REALLY needs to be turned off at night so we can sleep, and (if one cares about electric bills) anytime it's not about to be used. Sleeping/hibernating is not reliable on Linux still (in fact, does not work on this PC on Linux without major issues).
7) Applications. Linux has none worth noting that Windows does not have. Windows has boat loads that Linux lacks. iOS has boat loads that Linux lacks. The only thing that GNOME is good for to an average consumer is browsing the Web, e.g. light casual computing. Only, there are far better options than GNOME for that use case.
The most annoying part is, of course, that GNOME 3 is also just a horrifically bad tablet interface. GNOME 3's interface is a GREAT fit for netbooks, as its paradigms are a good fit for ~11"-13" screens, touchpads, and light computing. Too bad netbooks are already dying off in popularity thanks to iPads and Ultrabooks, and the market that remains is already filled by Chromebooks.
Also, yes, a lot of similar complaints can be made about Windows 8 and OS X's direction. The regressions are less severe in those cases IMO (e.g., Windows 8 loses the awesome Start Menu, but not the entire rest of the PC desktop paradigm). Maybe Windows 8 will be the next Windows Vista. Maybe not. In either case, GNOME isn't going anywhere new in the market that it hasn't already failed to go in the last 15 years.