The most basic web page development exercise - 1 browser window and 2 editor windows for html and css - is ruined because I can no longer MRU cycle the 3 windows.
I would say this is one of the biggest usability mistakes on the Mac. Sadly, Unity & Gnome 3 have both copied this. Meanwhile, I don't fight the platform but use it the way it was meant to be - keyboard + mouse. But I'll be shifting back to Linux or Windows for all non Mac/iOS development.
Update: thanks to comments pointing me to Witch. However, I still stand by my criticism of the built-in Mac desktop behavior.