I could try on Ellis' shoes for a moment, and figure out why he would take no issue with Cortana* and yet take issue with Quiet, it's about the appropriateness of the attire. For a moment, shed the semi-Victorian notion that the human body is necessarily sexualized (if that doesn't bake your noodle, you're not paying attention, but I'm going to keep moving): Cortana's appearance is appropriate. She requires no clothing for protection or comfort. Her appearance isn't necessarily sexualized; the very same features you'd probably call "sexy" are just as much a visual representation of nurturing. I'm not saying that's the idea 343 was going for with Cortana; you'd have to be pretty dense not to know how she would be received by many/most male gamers - but there's a fitness to her lack of (digital) clothing.

Ellis probably assumes Quiet is supposed to be a warrior, and what little she does wear seems to support that notion. That being the case, he probably sees her attire not just as a completely illogical and ill-serving choice for a warrior, but also a ham-fisted play at eye-candy. He assumes too much, I think; as RC and others have pointed out, there's quite possibly a very tactical reason for it if her very skin is her camouflage (not particularly novel, but kind-of cool). That being said, I wouldn't dare try and defend her look as being entirely tactical; too many of the details are indeed stylistically aligned with a more sexually suggestive motive, but I'd hardly call that disgusting.

*I assume he takes no issue with Cortana, because it would be pretty bold to strike out at Kojima for Quiet if he thought 343i was guilty of the same type of thing.