Having thought about this a little more, here's another reason I'm in favor in subreddits: they would keep people from seeing, or more importantly from voting down, posts which merely don't interest them. I think there are whole topics which don't do well because some people think "oh, this isn't relevant to me/less wrong"--but there's still a subcommunity here which is interested in exploring them rationally, and posts on that topic would be better served in a subreddit for that community. (I'm thinking of meditation, but I'm sure there are others.)

Or, to come at it another way, having a subreddit for a topic would allow people to explore it in more detail in posts there, without having to worry about keeping them readable for the LW mainstream. A post which is interesting and relevant to people who are curious about the rational implications of x may not be interesting and relevant to everyone who is interested in rationality at all.