My biggest gripe is that the home and end keys don't work as I expect anymore. In Ubuntu (and windows afaik), the home and end keys work in pretty much every app (terminal, editor, browser and pretty much any text field) for moving to the start/end of the current line.
One of the other frustrations, which isn't entirely OSX's fault.. is that the shortcuts in my editor of choice (jEdit) sometimes use command and sometimes use ctrl.
I'm not trying to criticize any OS in particular.. but I've personally found it incredibly frustrating. I admit it's probably just because of keyboard shortcuts I've used for years are etched into my muscle memory.
I can definitely appreciate that switching in the other direction is equally as frustrating.