It's not even that one particular movie can ruin the chances of other, completely unrelated movies. It's simply that the whole premise of 'rating' a movie based on specific content without any context is a stupid idea. So there is some nudity in Watchmen. So what? Do you think a pair of breasts is going break the fragile little mind of a 10 year old? Yes, I'm sure some people think that, but why should the nation as a whole suffer from it? Let them start their own, even more conservative rating system, one which the general public can ignore.
To compare things, I just looked up the rating for Watchmen in the Netherlands. It's 16, which is the highest rating we've got. (it's all, 6, 9, 12, 16) This isn't that unusual. For example, it was the same rating given to the Dark Knight. It's probably due more to violence than nudity.