Do you not admit that the permission system as it is does rely on registered as primary?
So, to make it more user friendly, my suggestion could be to make registered a compulsory primary a very definite default. But people can opt out of in special cases, e.g. make that a box they have to tick or something.
I don't want to make it dumbed down or less flexible - just more intuitive.
It doesn't rely on it, it's just the heavily recommended way.
There's nothing necessarily wrong, per se, with each group having their own primary user group and that being their only group, it's just more trouble than it's worth because when you want to change something, you'd need to change it and then remember to change it in the other user groups as well.