Continuing my response to this article I'm going to (briefly) talk about SEX!
Now don't get your panties in a twist, I mean sex as in the people we are, not the fun stuff. Discussing the Doctor regenerating as a woman is important from a feminist angle, but it seems even more important from a queer angle (note, I'm using queer here to describe all forms of what is traditionally considered "deviant" sexuality, that is, encompassing LGBT and anything else out there. I know it's not a perfect word, and it can be controversial, but for the purposes of being able to explain what I mean in a hopefully clear and concise manner I'm going to use queer as a catch-all).
If the Doctor were to regenerate as a woman it would do more than give the show a powerful female lead, it would give it an opportunity to explore and challenge conventional ideas of sex, gender, and sexuality. After all, isn't that what Doctor Who is all about? Exploration?
I wonder if some of the "The Doctor can't be a woman, it's not canon" and "The Doctor shouldn't be a woman the show would suck" responses come from people who don't want their ideas of what it means to be a gendered being pried into. When taken head on, sexuality becomes a hard thing to pin down; it's not as cut and dried as some folks want it to be.
Doctor Who has the potential as a piece of storytelling, to push people out of their comfort zones, to challenge their ideas of gender and sexuality, and do it in a way that is accessible to people with heteronormative view of the world.
One of the ways fiction, particularly speculative fiction, is effective is its ability to expose us to new ideas, to challenge the way we see the world and to do it in an empathetic and non-threatening way. I think that Doctor Who has a chance to do that, and the result would (if written well and handled correctly) be incredibly powerful.
More than anything, I would love to see a lady Doctor because it would blow traditional ideas about gender and what it means to be gendered out of the water, and explosions are fun.