They were the six main elements the Great Beings chose. The six primary elements lived in several places. There could have been a few other matoran living in Metru Nui, but not enough to warrant its own Metru. I don't think the other Matoran weren't allowed or anything like that. The way I see it is like where a lot of Italians live together in one spot, or a lot of Asians. They can live wherever they want, but they choose to live next to others who are similar to them, whether it be by race, interests, or jobs. (I apologize if that sounds racist. I'm not trying to be.)