There are almost no preferences at all. It automatically opts into the Lion-era autosaving and document-persistence garbage that I have no need or desire for, with no way out.
The text tool starts with "Text" in it, which has to be selected and replaced! What?! And instead of a default text style, it just uses the last one you used, regardless of time or document? And text attributes just overflow off the side of a document with no way to access them except to resize the window?
The effects toolbox could easily have been a dropdown menu instead of a huge, inefficient mix of UI pieces...
Effects and tools don't cancel if you try to select another tool... if I am in the crop tool and think "oops, I need to move that text," I have to hit cancel. Clicking anywhere but OK ought to cancel the action, but everything is greyed out instead.
I have to drag a corner in and out a little in order to reveal the ability to rotate with the cursor. Why didn't these controls show up when I selected the move pixels tool? Literally nothing shows until you try resizing the image, even though the resize handles are there.
Anyway, it's stuff like this, on and on, every time I try to do something, it's like they read my mind and do it a different and weird way that makes no sense to me.
Obviously this is just my opinion, though, lots of people seem to love it. But there just haven't been many options until fairly recently.