I'm actually posting this so I can reference it later if I ever get around to writing those articles for the Analysis section at GA. The outlook isn't optimistic, but you never know.
There was a lot of talk about Bayonetta when it came out; I haven't played the game, so I won't pass judgment on either the creator's intentions or what his work actually accomplishes - or fails at, whichever you happen to think. acebullet and I were talking about nudity in games and how exploitative it is in each situation, which naturally brought us to Xenogears because, as those of you who have played the game know, there's a lot of nudity in the game, both male and female. What inspired this entry was the speedo scene - not because it's exemplary of how well Xenogears handles nude characters, but because it's exceptional in context with the rest of the game for being considered either funny or disgusting by the fan base.
On that particular topic, we speculated the scene would have been more serious if Ramsus's sprite were naked; the speedo inspires eye-rolling, wincing, and takes away from the real content of the scene, which is Kahr's dream and the following conversation between Grahf and Miang. It can't be argued that nudity would be too explicit, because the game sprites aren't detailed or refined enough to pose a problem; secondly, the game doesn't shy away from the issue in later scenes at all. Both Fei and Elly, as well as Emeralda, are shown with no apparent covering at other points in the game.
So, I would say that nudity in Xenogears is entirely a spiritual matter. It's used as a metaphor for birth (of the individual, of humanity), intimacy (physical and emotional), and the individual's spiritual state, just as the presence of clothes in scenes depicting sex or communion with god is a metaphorical barrier, as in the Ramsus and Miang scene, or a later scene between Kim and Elly.
Here's a list of scenes I'm thinking about:
Scene 1: game introduction, Miang on the beach before she creates her first "children"
Scene 2: after Ramsus's dream; both Miang and Ramsus are in bed and undressed
Scene 3: Zeboim ruins; Emeralda is formed and stolen from her nano-tank
Scene 4: Solaris; Elly's shower, which both she and Fei use, but their figures are misted out
Scene 5: Taura's house; Fei and Elly are healed in nano-reactors
Scene 6: Yggdrasil; Fei and Elly finally come together; technically two scenes, before and after
Scene 7: Fei speaks to the Wave Existence; note the presence of clothing
Scene 8: Zeboim, memory; just Elly, but Kim is present and half-dressed
Scene 9: within Deus; the confrontation between Fei and Krelian, with Elly present but asleep
Scene 10: ending sequence; Elly is freed; Krelian appears to help them and apologize
Other: each form of the Nisan angels (cathedral, Merkava)
My memory of the game is slightly misty, and the memorial album doesn't show everything via screenshot. Let me know if I missed any. Ten seems like too perfect a number.
Anyway, in each case, character nudity seems to serve a kind of thematic purpose. Scenes one and three imply genesis or rebirth, literal both times, although there are also other implicit beginnings in those scenes (the beginning of the cycle of reincarnation, the plan to revive Deus). In every scene where Elly and Fei are stripped down together (four, five, six), there's some kind of emotional revelation going on as well; note that in scene eight, Kim's flashback, he's half-dressed, but she isn't at all (although I think she's covered, at least? again, I can't remember, and don't have a screenshot), which is the next point.
In scene two, Ramsus is wearing some kind of clothing; in scene eight, Kim is as well. In scene seven, Fei is shown dressed, even though in every other scene involving this kind of spiritual meeting, nobody is wearing clothes to my memory. In these scenes clothing would seem to be functioning as some kind of barrier - emotional, psychological, spiritual. When Fei first meets the Existence, just as when Lacan did, the meeting is incomplete because they need Elly.
Spiritually speaking, we have Miang's genesis, scene five, in which Fei and Elly both meet their memories of each other, the aforementioned scene with the Existence, and then the last two, in which Fei, Krelian, and Elly all confront the issue of their own humanity and the necessity of a god. In addition to that is the Nisan angels, which are always depicted nude, and symbolize the path to god. Considering all that, I'd have to say that while the character designs certainly exploit women if you want to look at it that way, the instances where people run around naked are completely serious.
There's probably more that can be taken from this, but I'm just stating the obvious conclusions, here.
Xenogears has more nude character portraits than any other game I can think of, which... amuses me. What a distinction.