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The fact that he is male is one of the defining characteristics, and has been the subject of plot-devices, jokes, relationships etc. Although biologically he could change, he shouldn't because it would completely change the dynamic of the show.
The fact that the character can be almost completely altered is what's truly interesting about the doctor. Certain plot devices and jokes won't last forever, and seeing the doctor from a female perspective has a lot of potential to bring something new to the show.
this does not mean that changes in the dynamic are bad, remember that this Doctor Who is a reboot, The show has already gone through a metamorphosis once already, not to mention each change of doctors/companios. Who's to say that a female doctor would be bad, it may be fun with new jokes and devices