I always find it confusing how people can prefer Xcode. I guess it's whatever you're most used to and comfortable with. Xcode does look a lot better aesthetically, but that's about the only thing I can think of.
IMO AppCode has much better code generation, refactoring and navigation. For instance, I've yet to locate a way to find all references to a symbol in Xcode.
I'm not "most used to" Xcode at all. I've been using Xcode in a hobbyist capacity for six months while I've been using IDEA professionally for four years.
Xcode simply feels like it belongs. It acts as a Mac app should act. AppCode doesn't; it's unpredictable, lacking in basic features like Counterparts, and still kicks me out to Xcode just long enough to remind me how much nicer Xcode is to work with. Code generation and refactoring is very pleasant to have but not as important as being comfortable to work in for hours at a stretch (and AppCode isn't worth the price just to employ it for a couple features for a hobby project).
IMO AppCode has much better code generation, refactoring and navigation. For instance, I've yet to locate a way to find all references to a symbol in Xcode.