I'm confused by his reasoning because there are female protagonists in gaming. I think I'd rather we keep male protagonists male and female protagonists female. If he wants his daughter to play as a badass female, he should introduce her to Metroid and Tomb Raider.
But she wants to play Zelda. The issue (if "issue" is even an appropriate word for it) isn't that there are no inspiring female characters, it's that there isn't one in the game his daughter loves. He doesn't want her to "play as a badass female", he wants her to see herself in the Wind Waker. There's nothing confusing about his reasoning in that regard. It's pretty straightforward.
Besides which, Metroid and Tomb Raider are very different games, in tone and gameplay and the level of skill needed to make progress. You can't go on a sea-faring adventure in either of those. You can't talk to your boat. You can't discover Hyrule beneath the waves. The idea that she should just play something else ignores the point entirely.
I've said for years that Zelda should give players a gender option at the start of the game. There hasn't been a single Zelda game yet that
needs Link to be male, and, honestly, the only reason anyone gives for why he should be is simply that he always has been. I know that it's tough to see a character you've known for years change like this, so I don't think that argument is invalid. I just personally don't think it's very strong, and certainly isn't a reason to not be more inclusive of a massive part of the fanbase. He'd still be male for those wanting him to be. Nothing is lost, but something valuable is added.
If someone wants to alter an existing game to suit what they want from it then go for it. Developer intentions mean exceptionally little to me. It's an interactive art form. Developer intentions are going to collapse they second they meet the player. And we have numerous ways to alter the experience built into games already. That's what difficulty options are. That's what an options menu is, and they're getting more comprehensive every year. People always have and always will tweak games to suit their needs and desires better. Hell, The Elder Scrolls series is mostly popular
because of people altering things to suit their wants. Changing text to make Link female is no different in that regard. It just requires more work, and I personally don't think it should.