OK, see, Joanna Lumley in "The Curse of the Fatal Death" is a good example of what not to do.
But I think a female Doctor could work very well if they do it very carefully. I've got this image in my head of Rachel Weisz as the Doctor and I just can't get it out. But the trick to making it work is that they need to un-sex the character. No skirts. No cleavage. She's cute and sometimes flirty without intending to be. (And when she intends to be, it turns out very badly.) She has about the same level of social graces as Matt Smith does. And while she enjoys this new incarnation, it still feels a bit alien to her if she stops and thinks about it for too long. (I have this long scene in my head where the Doctor first regenerates and realizes that something is different. She knows that she's a woman but can't quite put her finger on what the actual change has been.)