They could be badges from other gyms, like how Gary got ten Kanto badges (and he never got the Earth badge).
And N and Team Plasma need to get in the anime! I know Team Plasma was in an unaired episode where they battled Team Rocket in Castelia City, but it was deemed in bad taste because the earthquake happened just before it would have aired.
I want N to appear so badly! I just know he'll be super badass!
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