Considering how beloved the Miis are, they should definitely stick around, but all the more improvements they can make to them, the better. They should be central in our online identity - just as we have a Mii set as our personal identity on the 3DS too - and they should definitely make sure that they retain the kind of charm they have now and the same level of creativity in design.
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The new generation is, in many ways, Nintendo's to lose.
... wow. It's been said before, but you're really good! Set up a blog, or link us if you already have. I'd love to hear more from you.
Anyway, I'd love it if we could design our own clothes, Animal Crossing style, or if people could submit accessories, à la Team Fortress 2. Naturally, there'd be palette and polygon limits for the latter, but it'd be really cool (and a nice way of getting new accessories). Clothes, in my idea, be distributed with no quality-check review, in a big user store with ratings for everything, while accessories would go through an approval process (the first stage could be some sort of online user-run voting process). Perhaps users could re-skin accessories (similar to what people do on Roblox) and submit them to the user store.
Naturally, there'd be report buttons, checking for inappropriate art and words, and the like, but overall, it'd be really cool.
As far as keeping Miis goes, I'd say yes. They're a lot of fun, in my opinion. If you don't want to use them, don't.