Yup, I've talked about this a lot to some of the people building some of these things, and I am also convinced that HN like link aggregator type sites that are single community servers are better. There's one federating (Soon™) one called Brutalinks that looks pretty cool. I think the need to have multiple communities on one site is a unique need for centralized services like reddit, and something like categories and tags for different servers in a federation is the proper way to go.