I think it's just a problem that will work itself out over time with more users. There are redundant subreddits as well, but as the overall userbase grew only one or two subs maintained the subscriber growth to continue showing up on r/all. And in cases where redundant subs both grew together, they evolved to be very different atmospheres. For example, r/games vs r/gaming; one is focused on news and discussion while the other is mostly memes. Both great subs, but started out nearly identical until they found their identity.