Where I come from on this.
On modifying the game and 'violating IP': No.
I've
made a couple of games myself. I wrote the story outline (my partner did 90% of the actual dialogue, being the English major and all), set it up a certain way with a male lead. What if someone edited the game to replace the main character with the female co-lead, and put the male lead in it's place?
Well, I couldn't do anything really, and it wouldn't harm my original creation. The laws and understanding of copyright applies to making copies, not altering personal versions. The original game remains downloadable and available, and no other user copies are affected. This right is what allows
parodies to exist in media, for example, which are entirely dependent on being able to remix content. While they would have to spend quite a bit of time re-arranging the dialogue in my game to make it work, it'd still be well within their right. Could they re-distribute it as the "intended" game? No, copyright law protects my vision. You can't take a game, change the character, then claim it as the intended work. The father in this scenario is not saying you should play his copy.
On Link needing to be male:
Wind Waker's story has no reliance on Link's gender. There are no love scenes or direct requirements that Link be male or female. Link's appearance in the game is competely androgynous and in the chibi style. The game already allows you to change Link's name to something else, so nobody currently has an issue with the male Hero of Time being named Sue. Why not go the rest of the way and have people refer to the player in the gender pronoun they identify as?
On "losing" Link as a male hero:
This is the silliest reason I've seen, but one I've suspected and one finally mentioned in this thread. You do not lose Link as a male hero; your copy of Wind Waker remains unaltered. It seems people are more scared of the thought that changing Link to a female via a simple text mod makes him 'weaker' as a male character. This isn't a zero sum action. Now there's a tiny branch off everyone's interpretation of Zelda where Link is a female. Much like crossplayers ALREADY do. Nobody is saying women crossplaying Link are being mean to Nintendo, are they?
On "just go play ____ , it has a female lead"
Look guys. We have thousands upon thousands of male heroes and male leads in fiction. We have such an embarassment of wealth of being able to play male heroes, we don't even realize it. Not only are a lot of your suggestions outside of her age group and understanding, but this is what I describe as a "glass ceiling" type of response. This is telling women they don't need anything else to cater to them, "they already got a few heroes, isn't that enough?" Unless he wants her to play Super Princess Peach (ugh) or a Disney Princess / Barbie shitware game, the amount of female heroes for her age group in gaming are virtually non existent.
Male heroes for kids in gaming in actual GOOD games that NeoGAF would play: Mario. Link. Spyro. Banjo. Jak (1). Crash. Donkey and Diddy Kong. Tony Hawk. I could go on and on.
Female heroes: Nondescript female character in Pokemon.
Yeah.
"It modifies the original game, therefore it's bad"
In fact, this was already done to Zelda (since we're on the topic), WITHOUT any outside programs, just with inputs to the controller. Amongst other glitches that allow you to change the game's sequences or story. Someone has now modified the game to have Young Link be the victor at the end of the game of Ocarina of Time, not Adult Link. Other gamers figured out that a certain sequence will modify Halo 2's scripts and memory to prevent the second station from blowing up in the first level - a notable plot point, and one you can repeatedly execute to now alter the game to your taste each time you play it.
Or in less dramatic instance: Fan translations modify an original game, much farther than the father did. Ports done by an outside developer often change significant parts of a game, with no involvement from the original creator. Gamers often use Gamesharks, Action Replays, or trainers on PC to fly around a level, play as a different cutscene only character, or let you kill unkillable NPCs. In no way is the original creation harmed (it still exists and does not affect the owners of that copy). Especially in PC gaming, where there's a base rule that a PC game will at minimum have at least one mod available for it. Like Just Cause 2's flying mod, it's infinite rope mod, or say.. Counterstrike, an entire game made out of modding Half Life 1. Half Life and Just Cause IPs don't seem to be in shambles or burned to the ground, so I think they survived. (In short: everyone has the right to modify their copy of a game. But developers aren't also required to make it easy to modify, nor are they required to allow you to connect to their servers with your modified copy - that's their rights in play)
"What if someone changed Jade to a male so their boy wouldn't have to play as a girl? Wouldn't you be mad?"
It'd be interesting, but I couldn't be against it, since that would make me a hypocrite. But in the realistic sense, this is very unlikely to happen - males of that age group have plenty of male heroes to play as. They already have Link, they already have Gruff McBuff in Teen rated shooters. As males, we have so many heroes to play as that we DON'T need to modify anything to get access to a male fantasy. In a realistic scenario, and what actually happens: the parent just doesn't buy Beyond Good and Evil, or the boy gets disinterested and goes back to Zelda because he has a wealth of male avatars to use.
"Play as Samus!"
One of the more notable things about Metroid is that it was a "twist" at the end that the character you were playing as was a female. That should tell you right there that it's kind of a flimsy game to note as female-centric.
"Play Super Princess Peach"
Shut your goddamn face.