While Nintendo has always had a kind of gender neutral design in their games it has usually been a little on the "masculine" side of the scale, especially when it comes to the playable characters and some themes. It is nothing that is noticeable unless one mentions or analyze the product and it does not gravitate people away or makes them not feel included in the experience. So Nintendo has always done a great job in this department. Even when I doubt they thought about it.
What I have noticed recently though is the nature of their female aimed products, and this is the part where Nintendo stands out in a very positive way amongst the big companies in the industry, even the games which are "female" oriented are most often enjoyable for everyone no matter gender. And, most importantly, they are not just all pink, make up and tea parties (most often). Most other companies when making games targeted towards females makes an half-assed riding game or a tea party simulator or something like that which does nothing but over-generalizing and completely distances any male gamers from the experience. The only obvious game that is over-generalizing what is "feminine" and "masculine" from the Nintendo camp is Style Boutique. But even on Nintendo's own (Swedish) website they encourage guys to try it out and not judge it because of it's themes so they still show that very gender liberal approach about what is feminine and masculine which I like in Nintendo.
The difference between illusion and reality is vague to the one who suffers from the former and questionable for the one suffering form the later.