I wouldn't say that Quiet's character is shallow because of her attire. I actually really like Quiet. Whether or not that's a result of a personal bias because I really happen to like Stefanie Joosten is another story, but I digress...
As Chris has said, she is a complicated character, and she adds quite a bit to the story. Despite not speaking, she's probably the easiest character to read in terms of emotion. You can clearly see respect and admiration for Boss, in addition to possible romantic feelings later on. Although I personally like the fact that it's never so blatantly stated. It's a relationship that comes about from mutual respect, which is significantly more meaningful and engaging than her just being the girl you can "pick up" in the game.
That being said, Quiet was designed entirely for the sake of fanservice. This is just a plain and simple fact, and impossible to deny. She is eye candy. And with Joosten doing the facial capture, it's damn good eye candy.
However, I'm not so convinced this is a bad thing, in of itself. Is it wrong to treat women as trophies? To put them on display for men to enjoy? Well, sure. Women are people too. They have feelings and everything else.
Quiet, though, isn't just treated as an object. There are a lot of scenes that are obvious pandering, in addition to her idle animations within the ACC. What I think kinda makes this okay, though, is that Quiet as a character, is not weak, or being forced to arouse you. You wouldn't be able to hold her down and make her act sexy for you. You don't get to tell her to act a certain way towards you, or any other character. The camera angles during cutscenes may show off her assets, but Snake doesn't. And when Quiet does, it's because of Snake.
Basically, it works as a sort of pseudo-romance option in the game. The animations in the ACC, the shower scene, the rain scene, her ending... it's all unlocked by increasing your bond with Quiet. Check the guide for the idle animations too. You unlock them by becoming closer allies with her.
So it's Quiet doing something for Snake, whom she respects, admires, adores, and possibly even loves. And as Chris mentioned, Snake also does have a softer side during quite a few scenes involving her.
Is she over-sexualised? Obviously. Is her reason for being naked flimsy and inconsistent? Duh. But when she shows it off, it's no different from a real woman trying to excite the person she feels attracted to. And there's nothing wrong with that. Saying that Quiet is a shallow character because of her attire is the same as real life "**** shaming".
The way she's dressed isn't her character. It's her design. Two completely different aspects of the character. You can hate her design, but there's no reason to hate her character for it. Pretty sure people are taught from a very young age to not judge a book by it's cover. Quiet isn't slutty. She isn't weak. She isn't submissive. Nothing that her design (or people mad about it) would accuse her of being.
In truth, it's possible I'm giving Kojima way too much credit, and he might just be a quirky (if not a little creepy) Japanese game designer, but that might have been his intention with the character to begin with. He's well-known for his social commentary, after all.
I'd like to believe when Kojima said we would be "ashamed for judging her" that this is what he meant. Trying to look past the fact that she's obviously over-sexualised and see that a legitimately interesting character is buried underneath.
Again though, I might be giving him too much credit. He is kinda pervy.