I think most people by now have heard of awesome dad who redesigned the original Donkey Kong so that the princess can rescue Mario, instead of the other way around.
Now an animator has created a similar set-up for the original Legend of Zelda. The story behind the design is here, and it's a pretty awesome one.
These are awesome projects, and I hope that people continue to do them, and even that the modded codes become available for download (although that's very complicated, I'm sure). Even in Nintendo games like Harvest Moon, with any particular plot or relevance to the protagonist, it didn't become possible to play as a girl until quite recently (and some of those options were actually removed from the games before they were released here in the UK). As Tropes vs Women has already made clear, even in these unrealistic fantasy settings, the girls are always the damsels (or just plain not there), and the heroes are always male, even if they're not actually human.
You can't even play as a girl in Super Mario Brothers Wii, which has options for four players. There are at least two non-evil female characters in the series, yet players get to choose between Mario, Luigi, and two generic Toads. It doesn't make any difference to gameplay, but it does reflect the general tone of even non-character focussed gaming.
Meanwhile, there are now a few major series that feature female protagonists... but many players could be non-the-wiser about them. As far as I can remember, a player could go through the entire Portal series, and most of the Metroid games, without ever realizing that their first-person protagonist is female. If someone wanted to tell their child that they were playing as a male character, I don't think they'd encounter any problems.
It's all pretty depressing stuff. But hopefully, game designers will see this as more than a little novelty, and consider their female customers (both young and old) in the future. In the meantime, I'll keep playing my "design your own character" fantasy RPGs... and then spending hours trying to find suitable armor to match.