Some end up being minuscule (I'm looking at a ~1px-wide ownCloud icon right now) and the location is definitely non-obvious. I didn't even know Gnome 3 had a system tray for about a month, until I accidentally pulled it up.
> alt+drag to move/resize windows
This is not enabled by default, and there's no way to enable it in the default settings manager. I think gnome-tweak-tool has added support, but I had to dig around in dconf to enable it not too long ago.
> even alt+tab don't work out-of-the-box
Alt-Tabbing in Gnome 3 is fscked. You're expected to use Alt-~ to switch between windows of the same "application," while Alt-Tab only switches between application-group-things. You can fix it with a plugin, but you have to fix it with a plugin. That's ridiculous.
> Window focus seems completely broken
New windows are sometimes raised above other windows. Sometimes they're raised below. Sometimes they have focus. Sometimes they don't. I've experienced this issue with other window systems too, though, so I don't know if Gnome is to blame for it.
> more often than not, their way has turned out pretty good
It's something of an 80/20 scenario: yes, most of "their way" is perfectly fine, but a good chunk of it just sucks. Worse, which chunk of it sucks is different for different people and for different reasons. For example, I can't stand workspaces, but I know people who swear by them. Conversely, a lot of people prefer the old program menus, but I like the incremental search Gnome uses.
This is a universal problem, and it's easily solved: give the user options. No matter how well you design an interface, it's going to be wrong in some way for someone. By all means, yes, ship sane defaults, but give your users the ability to control their workflows on their computers.