I know I'm going to be railroaded as an apologist for Ueda, but the fact that they even considered a female lead is actually pretty progressive for the video games industry, to be brutally honest.
In my humble opinion, I support the choice of a male lead, if only because I strongly identify the "Boy and His Pet" theme that TLG seems to be trying to convey. Objectively, nothing's changed by making the protagonist a girl, but if you're looking at the demographics, the fact remains that you're mostly delivering to the XY chromosomes.
So while I'm certainly not going to discourage developers from nurturing more well-developed, stereotype-defying females, I can't exactly blame them for playing the numbers game when it comes to the business of these multi-million dollar games.