I do wish we could filter friends into list though. Also having people's Mii characters listed isn't going to be helpful, since some people name them after themselves. Not many people are on a real name basis and it might be confusing if they know someone else with the same name. Though the name input section isn't big enough for some forum names so they'll have to be shortened.
I primarily record people's Miis that are specifically tied to their system so that they can associate who's who from the forum if they didn't add each other immediately. An example would be like me registering you, but you haven't had a chance to register me. I have you identified by your forum name in my system until you register me. When that happens, if your Mii has a completely different name, I can always refer back to this thread to see who exactly it is on the forums.
You are right in that people can have the same exact names in the system and, as far as I know, there is no way to add notes to peoples friend's cards in your list. I hope that they will add something like that in the future. But aside from that ( and the ability to separate those who haven't registered you vs. those who have) I'm pretty happy with the system in place...so far

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