The interesting thing about the title 'doctor' is that it is, theoretically at least, non-gender specific. Society has moved on a bit since then, though. It really shouldn't. The whole process of regeneration is ready-made for an explanation of gender change. Contemporary sci-fi writers have addressed the issue in a number of ways.
Consequently society finds it difficult to describe women apart from their sexual function.
Both approaches satisfy the ever-present desire to define women in relation to their sexuality. The same desire does not exist in respect to the representation of men. Now, if we change the gender of the Doctor, the real root cause of all our misgivings is that the makers of the programme will, consciously or not, fall into the old routine of having this female Doctor, at worst fall in love, or at best play on her sexuality, every episode. There are two ways to approach this. After all, McGann's Doctor has already shown more than enough interest in things sexual to set a precedent for this type of thing.