Yeah I could buy it if the Time Lord's did see gender differently to us and didn't really care if they regenerated as male or female, but all evidence so far is that they don't, their biological sex matches up every time with how they self-identity?

And right, I can understand feeling like it would be an important and progressive step to have a female Doctor, but does that mean that it would work in the continuity of the show? I'm not as opposed to it with film characters like Bond actually (although I'm not familiar with the source material there either admittedly *g*), cause every film is kind of its own version I believe? But for a continuing story like Doctor Who, I do question how it would work for an established male character to choose in-story to switch to female. It worked with Missy of course, but as you say, there are still questions there as to why the switch, it's a pretty out of the norm event within the show