The single greatest failing with Quiet is that Metal Gear Solid used to write incredible roles for women, especially relative to the years they came out. They were data analysts, they were spies, they scientists, they were doctors, they were soldiers, they were weapons experts, and they had goals and ambitious and purpose beyond titillation. Metal Gear Solid, the first game in particular, wrote the kinds of female characters you couldn't find anywhere else in gaming. While there were still sexy characters like Sniper Wolf, they were not without their characterizations and they were counterbalanced by a large cast of well-written women.
As the series went on, these kinds of roles decreased. They were written out or given to men. By the time we get to Metal Gear Solid V, the most prominent (and one of the only) female characters in the game is a nearly-nude honey pot who literally does not speak. She is there to be seen, not heard. In a story about soldiers and corruption and dark actualization of wartime politics, the lead female is relegated to slinking around in the rain. Nothing about her design is justified or makes sense in the context of the story and it sends a message. It tells women that these stories are not for you. They're for boys. While all the male characters are there to tell a meaningful story, Quiet is there to crawl around in a bathing suit.
So yeah, of course Kojima can tell a story about whatever he wants. There aren't rules about what kinds of stories people should tell. But it reflects poorly on Kojima that this is his idea of a meaningful female character that will make us "ashamed of our words and deeds." It's embarrassing. I don't fault you for liking Quiet. Quiet exists, she's out there, like her or not. But it's very unfortunate that a series once famous for women in STEM now focuses on sex objects who can't talk.