To be frank, Raiden wasn't naked the whole time in MGS2. That wasn't his actual, default look, while Quiet's look most likely is. The part where Raiden's actually naked is very short and obviously a gag, with a bit of fan service. Quiet's outfit will probably be like this for most of, if not the whole game. But then again, MGS games have had a lot of fan service and sexual themes which, in part, is prevalent in Japanese games and anime anyway.
However, I really don't see that much of a problem in Quiet's outfit and there will most probably be a lot of abuse and degradation in her backstory which drastically affected her psyche, rendering her unable to speak yet she expresses herself and her revolt through her looks and her weapon, the sniper. That, with a combination of needing to expose her skin for photosynthesis can be somewhat of a good enough reason for her too look this way. I mean, it's all on par with Kojima's earlier characters and themes, it's just that they all look a lot more photorealistic in MGS5, so I guess it causes more of a stir.