I gotta say, I find this whole discussion kind of weird, because I have never felt that the gender of the protagonists of any given story had any meaningful impact on my enjoyment of said story. Nor did I ever have a problem playing a video game character because of his gender, because, honestly, there's a lot more to life than what is going on in your pants. I'm a big fan of the Wario Land franchise (duh), for example, and Wario is probably the least feminine character I can think of. Still, I enjoy playing as him, because he's an awesome character, and really speaks to the worst sides of my nature - I mean, who doesn't like to play as a greedy, immoral, selfish slob of a man who doesn't have an ounce of heroism in his body and is just doing it for the money? I definitely get a kick out of it - and yet I'm very different from Wario, and not only regarding my gender. (Or at least, that's what I like to tell myself.)
In the same way, I have taken on the role of a genetically enhanced bounty hunter in Metroid, a space-travelling plumber in Super Mario Galaxy, a vertically challenged boxer in Punch Out!! or some cutesy aristocratic brats in Fire Emblem. And guess what, none of them are like me in reality. I have never morphed into a ball, I suck at plumbing, let alone flying through the galaxy, and even Glass Joe would probably have a good shot at knocking me out.These characters aren't me, and don't have too much in common with my real life; I doubt that Samus Aran wakes up at night thinking about her crippling student debts, nor could I refrain from complaining every five minutes if I had to put on some armour to help some fancy prince like Marth reclaim his monarchy. And you know what, that's totally fine with me! Because, in the end, I still enjoy their games. I feel like a badass when I kick Ridley butt, I'm as ecstatic as Mario when I fly through the star-filled depths of space, and when I'm finally able to convert some jerk's face to a bloody pulp, I really feel like I went through the same exhausting training regimen like Lil' Mac to achieve that. I share their experiences, I can get behind their goals, and I root for them to succeed.
And with Link, it's basically the same thing. Despite being so often dismissed as a blank slate, he is a character. True, he's not a character fitting the modern narrative tradition with it's emphasis on inner psycholgical conflicts and reactions, but more of a character in line with the pre-modern epic narrative tradition (think Beowulf, or, in the 20th century, Tolkien), that is, defined by his actions. He's the guy who looks at a towering pig monster and thinks "Yup, gotta take this thing down, there's a princess to rescue." He's the guy who, despite growing up on a far-off island without ever seeing anything of the wider world, sails away with some pirates when an effing giant bird kidnaps his sister. He's even the guy who will clean your health hazard of an apartment for nothing but your (crystallized) gratitude. I certainly wouldn't do that, trust me. Back in OoT, I would have repeatedly shat my pants after barely having survived meeting Gohma, and then hid under my bed until Ganondorf makes sawdust out of Kokiri forest. Not Link though, he's a courageous mofo who wields badass swords and unhesitatingly goes to places I would avoid like the plague, just to save princesses and siblings and kingdoms and stuff. And that's his character. I'm just along for the ride.
Thus, from my own experiences, I can barely relate to that guy, or any video game character. They are not like me. Still, I can empathize with them (yes, even with those gross boys). While my own interest in kingdoms and my desire to get in Zeldas pants is marginal at best, like Link, I prefer my towns filled with people rather than with undead hordes, I do think that a moon crashing down on a populated planet is an unfortunate event, and hey, Link seems like a nice fella, so if he wants to get some smooches from Zelda/Malon/Ruto etc., good for him! I do not need him to be a carbon-copy of me to take interest in his adventure, and I certainly do not require him to have the same genitals as I do.
So, what would having a female Link achieve? Would it make her more relatable? Not exactly, because while sharing my general biological set-up, female Link would still be a very different person. I'm staying under that bed, thank you very much. And, seriously, I sorta doubt that most female gamers are the kind of people who would willingly battle with heavily armed megalomaniacs like Ganondorf for a living. There's always a disconnect between the heroes of our video games and ourselves, because video games usually let us experience adventures that we don't encounter in our own lives (unless you really enjoy playing Cooking Mama), where the most frightening boss enemies are those damn monthly bills. They are stories, and the beautiful thing about stories is that because of them, we can experience other worlds through the eyes of other people. When my dad read the Hobbit to me when I was 5, I was as scared as Bilbo as he encountered these cockney-speaking trolls (more because of the troll part, not so much because of the cockney), and I wasn't egotistical enough to demand that Bilbo could have at least worn the same pigtails as me for the occasion.
Because that would rob the character of his autonomy. And yes, even Link has that autonomy, acting and reacting in his own ways, having his own self, his own background and story, established over multiple installments. True, in a video game, I do have control over what he does, but within the limits of the narrative. I might be a psychopathic chicken abuser, but the story has tactfully ignored this unpleasant fact so far, leading Link to heroically saving the world again and again. And that's canon, folks. Changing his gender would throw all of this canon away, reducing him from a somewhat shallow, but good natured bloke with an impressive resumé over his several reincarnations to an idealized version of myself with an uncanny fascination with green fashion disasters. And why? Because balls.
(PS. There's a certain irony to the "But Link has no character" argument, by the way. I don't want to go into depth here, because this post is getting rather long, but reducing Link to an unspecific avatar character would be a surefire way undermine any of efforts to give future Zelda titles more story development and deeper characterization. And frankly, when it comes to getting better games or having more of mah female representashun, I choose the former.)