Something about making the Doctor a woman seems like it would just be pandering or doing it for the sake of provoking controversy. I don't know that it would add anything to the story to make the Doctor a woman other than spending a lot of episode time going over how crazy it is that she's a woman now, and isn't that new and different. That does not strike me as particularly compelling, compared to the rest of what makes Dr. Who an entertaining series.
To me it seems like saying "What if we made the next James Bond JAMIE Bond." Sure, you could do it, but would it add anything to the series? For my money, no it wouldn't. The companions (at least in the new series, I can't say much for the old) are far from damsels in distress. There are plenty of strong female characters, and making the iconic Doctor one of them just for the sake of making him a female seems silly to me.
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