I think it's funny that the article plays the "princess dresses differently to have a life outside of the confines of her palace!" plot as somehow making a point about gender issues. It's reading way too much into the material than is useful or even meaningful.
The deal with Zelda goes in the same direction of Samus' problem in that Zelda has to assume a different identity to actually do things that she may as well be able to do WITHOUT pretending to be a man/not herself. Samus' case was of course that the fact that people were surprised the guy in Metroid was actually a girl cemented the "Oh wow, girls don't really do that!" mentality. Otherwise, why even bother with the surprise to begin with? I mean nowadays it's a moot point considering everyone knows (and it gets milked for all the fan service possible, of course, just like you'd expect from a female game character.)
But then again, it seems to me the whole article is focusing on a particular franchise that has never been really that creative with gender roles to begin with. It would've been much more interesting to see more exposure to other games/characters and treatments of the same issues. However, I do think that the issues of gender are often nothing but caricatures whenever they're found in games. Yeah, maybe the topic can be alluded to or even show up directly, but doesn't mean it has any weight or consequence.
After all, for all the article talks about Sheik, she's nothing but Zelda's "cool sexy" mode now, much like Samus' zero suit nonsense. That is enough to signal how little point there is in trying to find any depth into that franchise or character when it comes to issues of gender and/or sexuality. Like I said before, even in OoT what they were doing was nothing new at all and actually an established plot with thousands of examples across all media.
If anything, we can use this article as an example that if people are overanalyzing something like this, trying to find the slightest hint of a mature topic to discuss it simply means that there's a general lack of maturity in the topics dealt with in the medium. This is of course nothing new and no surprise to anyone who sees the progression "to mainstream" of all these characters and franchises.
In that sense, expecting any games produced in that direction to deal with issues that require a certain level of intellectual maturity and cultural knowledge is hopeless. Maybe we'll see it as the culture in general becomes more accepting/open with the issues, but honestly I don't have all the time in the world to wait seeing that the real reason games are stuck so far behind is simply that artists/intellectuals/etc from other fields haven't really taken interest in the medium. I'm not talking about the gaming "industry," either, I'm talking about the medium in general. It can't mature if it's so completely isolated from the rest of the arts.
It's really an understatement to say that the medium as it is right now is in its infancy; I'd say it hasn't even technically been born. Not until it acknowledges the wealth of film/literature/music/etc around us in a meaningful and consequent way so that there is an exchange/flow of ideas will the medium attract people willing to take risks and make use the medium as a tool of expression. Only then, really, can we begin talking about the treatment of complex issues like gender identity or sexuality in games seriously, and not simply pretend that only because a game displays a set of breasts we have free pass into discussing sexuality in any depth while feeling intellectually smug that "our" medium is "mature," which I suspect is the general sentiment concerning efforts like this.
Further reading concerning the actual trope behind Sheik I mentioned at the start (and she's even mentioned there!) http://tvtropes.org/pmwiki/pmwiki.php/Main/RebelliousPrincess
Yep, that's all there really is to it.
