http://terribleminds.com/ramble/2013/06/03/why-its-time-to-genderflip-doctor-who/From that article:
"The Doctor is practically already without gender. The romances are barely that; the sonic screwdriver is not a metaphor for some dude’s wang."
Except for the fact that romance, and sexuality and sex DON'T equal gender. You can be a bloke, and like men. You can be a bloke and like women. Liking the same gender as you doesn't depend on what gender you are. The fact you like girls is just that. That you like girls. Does it matter if you're a dude (making you straight) or a gal (making you gay)? You're still a dude or a gal. And you still like girls. Gender Identity is not our sexual identity. Just because the Doctor doesn't flirt, doesn't mean he doesn't consider himself a man. It makes him an asexual man, if anything.
There has never been any hints that the Doctor thinks he's a woman, or effeminate or is in the wrong gendered body. Time Lords/Ladies have never shown to be anything other than Male or Female (even if they're slightly different to how we'd class them). Romana didn't even consider a male body when she flipped through choices, even as a joke. When the Doctor was offered new bodies when being forced to regenerate from Two to Three, he wasn't offered a female body. Which says to me that Time Lords/Ladies have just as much as sense of in-born gender identity (male or female) as we do. We just know what we are. However, they at least get the option of forcing a regeneration and choosing a female/male body the next time.
Any other thoughts from you guys on the topic?