I've been using Linux of some flavour at home for the last 15 years, only straying onto Windows for gaming. I've been lucky to use Ubuntu at work for most of my professional career too (6-7 years?) - so it's what I know and what I'm used to.
I started a new role a few months ago that forced me onto OS X and found physical and software issues. Physically OS X does not let you configure mice properly without installing third party drivers. Of course I ditched the "magic" mouse pretty quickly after my hand started hurting after a couple of days, but even with a normal mouse you simply cannot configure mouse sensitivity and acceleration properly - it cannot treat a mouse on par with what Linux or Windows will. You need extra drivers to even enable mouse buttons 3,4 and 5.
The keyboard shortcuts hurt too, sometimes using Ctrl, sometimes using Cmd, but that could be just fighting 15 years of muscle memory - so take that with a grain of salt (but it indirectly caused more physical finger pain).
Software-wise I don't know how objective I can be, but it feels faster/simpler to install software and things like the terminal are much better integrated - I can auto-complete git branch names on the command line for instance. Maybe OS X can do that kind of thing, but certainly not out of the box. To me, OS X feels like a 95% emulation of Linux, just that slightly bit lacking.
Then there are the embarrassing things like I couldn't find the shortcut to go to the end of the current line. On Linux it's the End key - on Mac I assume it's some combination somewhere.