I've sometimes made nods to concept over mechanics, for example, spending a skill point every level in Profession: Orcish Barbacue for my half orc alchemist. I think doing so is a good thing in general.
However, with a half elf witch I'm designing, I found myself spending both traits on concept to give me the skills she needed to survive in such an environment (bluff and sense motive) raised by an abusive mom, a winter witch, who raped her father and then sent him to the bone mill. I found myself picking the ancestors patron (i.e. father) and was considering elven spirit as her first feat or getting extra traits to get the other things I need.
Basically, I found I was using everything to justify backstory and wasn't optimizing as well as I could/would normally do.
I'm considering dropping the character concept because I was using so much on background. So my question is, to what extent do your characters use thematic choices over the 'best mechanical option'.