- one menu bar for active applications: if you have many windows/applications open side-by-side you can't access (or even see) their menus until you switch to them. It's bad on a MacBook, I can't image the pain it is on a 27" or 30". If you're using Adium on a 30" monitor and you have it in the lower right-hand corner, the app's menu is 2 freaking feet away from the app!
-cmd+tab switches apps, not windows. you have to either use expose (slow) or cmd+tab, cmd+~. Minimized windows also don't cycle, so you can alt-tab to an app and still not get any windows, just the menu bar. Getting to a particular window shouldn't be so damned hard.
The windows/linux way - where each window is independent, equal and self-contained is much better IMO.