Nudity itself is not a goal, though if it complies with the storyline and fits in naturally then there is no reason why it should be limited or not used. Sex/nudity are a natural part of human behaviour, and as long as the focus of the game isn't on the nudity, but the nudity further propagates the plot, then I have no problem with it - I would actually say that I encourage it.
There is naturally a problem with it - it tends to cause panic among concerned parents and the media, and thus heightens the rating level, making the game unacquireable for younger members of the gaming community - though I personally think that shooting someone's head off with a steam powered gun that shoots six inch railway spikes at point blank requires more of a "Mature" rating than what the implementation of some nudity would recquire.
I'm not asking that games are turned into some erotic form of entertainment, just that it finds its natural place, and that it isn't stigmatised as "unproper" or something along those lines.