Chromosomes. This is my theory/explanation for why all the Doctor's incarnations have been male, so far. If you were born male on Gallifrey, then most or all of your regenerations will be male. If you were born female on Gallifrey, then most or all of your regenerations will be female. Before you start reminding me of what Missy said to Clara in "The Magician's Apprentice" about him being a little girl. I believe that was the lie.
Missy: Which one was the lie?
If it were true, then the incarnation line up would be like this:
1. Little Girl
2. Hartnell
3. Troughton
4. Pertwee
5. T. Baker
6. Davison
7. C. Baker
8. McCoy
9. McGann
10. Hurt
11. Eccleston
12. Tennant
13. Tennant duplicate created in "Journey's End"
14. Smith
15. Capaldi
Now, you see why I think Missy was lying about the Doctor being a little girl. If it were true, the Doctor would've needed a new set of regenerations at the end of "Journey's End" just to turn into the Matt Smith Doctor at the end of "The End Of Time", let alone to turn into the Peter Capaldi Doctor at the end of "Time Of The Doctor".