OSX seems far too opinionated on things. It keeps installing Itunes even though I've gone through and deleted it repeatedly. It won't let me uninstall all of the Apple software that I have zero use for (I have no use for a word processor suite). I spend 100% of my time either on Firefox, Thunderbird and the Terminal. I have nearly zero use for any other gui applications and would like to uninstall everything down to the bare minimum of applications and processes to do my work.
Too many terminal applications are subtly different between what I have available on Linux vs OSX, and I'm frequently having to resort to compiling them myself to get feature parity. Shell scripts need to be every so slightly altered to account for the fact that its running on OSX and not Linux -- I'd like to be able to write it once and then run it on my dev machine, virtual machine, and server without needing to make these changes.
OSX likes to liter hidden files all over the place that I need to remember to exclude from git repositories.
These are all little things, but they're little things that have grown over the years to really irritate me and I probably won't be doing a MacBook on my next upgrade.