My personal pet peeves about Unity:
1) Half-assed implementation of application switching - especially / mostly when dealing with multiple windows from same application (TERMINALS!!)
2) System-wide menubar (and I'm a long-time Mac user, for chrissakes!)
Now, let me elaborate on both of these. I admit I haven't yet mucked around with settings, and I'm actually using unity on a University lab computers where BOFHs are mostly responsible for the state of things, so reality might not be the same for you:
1 - application switching: Previously, every window of an application was a "program" in it's own right for alt-tab switching. I could switch to whatever window I exactly wanted to, quickly. That quickly is a keyword here. Because now, if I want to get that-one-terminal-I-directly-want, I have to raise the application switcher on screen, alt-tab on it, WAIT FOR A SECOND, and only THEN I get to actually choose the exact terminal I want up.
On Mac (up to 10.6 at least), cmd-tab raises all of the windows of a single app up. Even THAT would be preferable to Unity, because then I at least I get the terminal I want quickly and smoothly. That wait, as short as it is, is infuriatingly jarring and I can't fathom how anyone claiming to be UX engineer would come up with it. App switching happens all the fucking time and introducing a jarring delay onto it is unbelievably stupid. They also decided to get rid of the win95-style application switcher, so I can't even choose my exact program instance from there. Gee, thanks a lot.
Then there's the fact that this stuff doesn't play nice with multiple workspaces/virtual desktops. Try launching an instance of a program on another workspace when you already have one open on somewhere else, you'll see what I mean.
2 - System-wide menubar: Well, I kind of get what it wants to do. But let me say it, it's a stupid idea. It was and is a stupid idea on Mac, and it is stupid idea here. It really only works on a premise you always use every program in maximised window. On Unity, it's made even more stupid by the fact that it's hidden by default and you only get to see the menu by moving your mouse there. So if I want to select something from the menu, I need to move my mouse over there even before I can move my mouse over the exact menu I want to use! I know, this is a small issue, but still. When you're mucking around with user interfaces, these small things MATTER.