As mentioned in a comment before I got here - Missy. We've had a Time Lord turned Time Lady, we just haven't gotten there yet in our watching.
Aside from that, I can also see this topic from the perspective of too many years of scifi fandom. This was explored in an interesting was in DS9 with the Trill race and how it affects gender and sexual preference.
But let me be arrogant for a moment and theorize that the reason it took the doctor 12 regenerations to become a woman is that perfection takes time. And so Time Lords aren't randomly assigned a gender at regeneration, but rather born with a gender according to their age and/or wisdom. Sure, it's probably just my girly arrogance, but this is a scifi show about a regenerating time traveler in a police box so I am going to go ahead and pretend. Because I can. :P