I'm not saying it's right, but Kojima comes from Japan.

They have a... different way of handling sexuality in their media. Looking at Quiet from a western perspective, yeah she sticks out like a sore thumb, all of the complaints are valid. Looking at the same character in the context of all the other stuff you see coming out of Japan, it doesn't even rate a mention, it's super tame. It's not even the only one to use human photosynthesis as a reason to take off clothes, Knights of Sidonia already did it a few years ago (though I think they were more tasteful about it).

If there's one characteristic about Kojima that defines his work, it's not that his ideas are especially outlandish or innovative in comparison to his peers, it's that he gets his way. He has a specific vision for his work, and he has the force of will to make sure it comes out exactly the way he wants it. At this level of AAA development, there's always a ton of people, including bosses, telling the lead developers "No, you can't do that, and here's a long list of reasons why", and Kojima is notable for being able to doggedly fight these people off to realize a highly personalized game in spite of the many people involved. For better or worse, few games at this budget level manage to maintain a single person's vision all the way through to release.

So with regard to Quiet's depiction...it's just Kojima being Kojima in a way that only Kojima can be.

EDIT:

To elaborate my feelings on the depiction of Quiet...I think this is really just symptomatic of a greater trend in Japanese media. Audiences are too forgiving of willfull and blatant usage of tropes. I enjoyed shounen-style anime when I was younger, it was definitely cool to see young teenagers getting powerful and depicting wish-fulfillments of power and "harems". But I've aged, while that industry is still very reluctant to age with me. Possibly due to the problem of high unemployment in Japan leading to a lot of young men who are stuck living off of their parents, and become otakus that never left home to mature into adults. Thus the industry has a large audience of high-consumption adult customers whose tastes haven't evolved over time as they grew older, and as such this industry has much less pressure to keep evolving the kinds of themes they present. This industry's heaviest spenders are going through a state of arrested development, and that influence is transferring to the producers of content for that industry.

For a constrasting example, I'm sure you're all familiar with the "Dadification" of games in the west, where the protagonist is now in charge of protecting little sisters, or Ellie, or Elizabeth, etc. It's due in part to the developers growing older and wanting to create works that represent in part the new feelings they're facing as parents. They're not at an age where they're trying to "get the girl" or "come of age". At this point in their lives they're already "of age" in a successful career path, and they've already married and "gotten the girl", and now they're starting to fantasize about being a good parent. Sexy girls are still sexy even to older married men, only now that older man now occasionally worries about his daughter lacking inspirational female characters that are more than just their sexual appeal. The average age of gamers continues to rise and right now the average gamer is probably a young parent with a job and responsibilities. Though there are still definitely games that are made specifically to target kids/teenagers, the western game industry has been growing to ALSO include a lot of content targeting older customers.

So with regard to Quiet, she's just "fan-service". It's extremely common for japanese media to break from the natural evolution of a world/story in order to squeeze in a sequence that is just to titillate and appease the fans without really progressing the story or building the world. Fan-service typically comes in either Action or Sexual flavors. Continuing to use MGS as an example: The series includes insane over-the-top action sequences that look cool...but also break the cohesion of the world's rules. For example, Solid Snake is kind of a worthless piece of shit being just a regular soldier firing small-arms, and running and crawling around on the ground, while he's contemporary with characters like vampires, invincible giants, soldiers whose fortune magic makes them immune to gunfire, ultra-agile cyber ninjas that can battle 2 story military mechas in melee combat. When the game gives these other characters a chance to do ultra-crazy feats of power to make them seem cool and titillate the fans...it's also undermining the idea that Solid Snake could credibly stand toe-to-toe with them, making your in-game victories over these overpowered characters seem more and more like acts of extreme deus ex machina or blatant Bond Villain Stupidity, where they grossly underutilize their abilities only to allow oppportunities for Snake's incredibly limited abilities to overcome them. That's action fan-service that looks cool, but ultimately makes the world less consistent, less real. I'm not saying the MGS's military theme must have strict adherence to real-world physics, that's excessively constraining on the imagination. Rather a story is made stronger and more immersive when the fictional breaks from real-world physics remain consistently applied throughout the story. Immersion is broken when the audience sees a major character severely injured by a cutscene bullet even though these characters have already survived being shot with hundreds of regular bullets.

As for Quiet, she's the vehicle for sexual fan-service. If she was able to wear clothes like a normal human being, then the focus would not be on her tits and ass, instead other characteristics would need to be offered up to keep up the audience's interest. Her lack of clothing is distracting and immersion breaking and ultimately serves to undermine the realism of this world's fiction. But the sexual fanservice is still left in there to please a less discerning audience that prizes the sexual thrill above the immersiveness of the tale being told.

There ARE examples in Japanese media of more mature stories that have resisted the perceived pressure of needing to offer up fan-service in order to retain interest (like say, Honey & Clover), the problem is that this kind of storytelling is growing so slowly. I hate to compare cultures directly, but it's hard to shine a light on this issue without a contrast. In the west, instead of the inconsequential high fantasy of the forces of good overcoming the forces of evil, the most popular fantasy story we've got going on right now is Game of Thrones, in which the author doesn't provide characters with plot armor, avoids writing Mary Sues, and the events of plot progress organically along the groundwork of personalities and forces that have been set in motion, rather than allowing deus ex machina interfere constantly to ensure the happiest of outcomes in all circumstance. Even Harry Potter, which starts out appealing to children/teenagers, over the years the characters aged, and the atmosphere of the story has matured alongside it's readers. Similarly, popular works like 24, Battlestar Galactica, Walking Dead, The Road, etc. demonstrate that there are audiences that enjoy seeing shows where consequences follow actions and although it's too much to expect these works to be free of tropes, the audiences still enjoy the surprise of seeing these tropes being broken by writers that are consciously taking efforts to avoid falling into the trap of these tropes. Unfortunately it seems like Japanese media doesn't have the same pressure from it's audiences to buck their tropes, and it's evolution is slowed as a result.

I still enjoy Japanese media obviously, that's why I keep watching. It's so creative in other ways that it's hard to stay away. However, at the same time I think that some of it's potential is being wasted by not marrying these fantastical ideas to more mature writing.