I don't entirely agree with the man regarding haxing a game to tailor it to his child. Maybe I'm just jelly of his ability to do that.
There are simpler ways [I'd argue] to encourage his child. He could write a children's story just for her. Teach her to make things up for herself. The people who make things like Zelda got started by creating things that made themselves, or close friends, happy..
The problem amounts to this: The game pops up and asks Dad and Maya what to name Link. Dad asks Maya what they should call their character, since they can pick any name they want. Maya says, "Maya, like me!"
Does Dad then:
A.) Use the name Maya, and just keep calling Maya a "he", leading to "But Daddy, Maya's a girl's name!"
B.) Tell Maya, "We can't do that sweetie, this is a game about a boy." thereby diminishing (however slightly) her sense of engagement with the game.
C.) Say "Okay", name the character Maya, and just pretend the androgynous self-insert character voiced (IIRC) by a female is, in fact, a female, doing roughly 0 damage to the story of Wind Waker?
There's nothing to say there aren't other things he could do as well, but Wind Waker is a game that is very visually appealing to young children (it's lol kiddy Celda after all), and there aren't a ton of good substitutes out there for that experience. This is probably not the only interaction he has with his daughter, and they probably do many other things. It's just the objection people seem to have to him doing this small thing, giving his daughter a custom game experience tailored to make it the best possible for her, that baffles me.
Edit: It kind of reminds me of the granddad reading the story to Fred Savage in The Princess Bride. The story the kid hears is tailored to what he likes, parts are omitted that he finds boring ("the kissing stuff"), but in the end they have a good bonding experience. Fictional Granddad totally altered Fictional Morganstern's story, and probably could have picked a better Fictional Story to read to a sick kid that would have required no alteration, or written his own, but the end result is something special and sweet.