A female Doctor definitely ought to happen at some point. I don't think there'd need to be a specific storyline for it. It'd been well-established by this point that Gallifreyans can change sex when they regenerate.

For me, the 'the Doctor's always been x' argument is flawed, at best. Before Eccleston, all of the Doctors had accents from the South of England. Does that mean that Eccleston's Doctor was less 'Doctory'? Of course not. There's no reason a female Doctor would be any less 'Doctory' than a male Doctor.