The official japanese site for Best Wishes has just updated with the new look for Team Rocket. This puts them plus in-line with the Rocket Grunts within the games wearing black costumes. In Best Wishes, Jessie & James are classed as Team Rocket's Advanced Troops and are frontline for Team Rocket in Isshu for Giovanni to help Isshu fall to Team Rocket.
(Thanks to Sabonea Masukippa for the translation)
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Another article: ozymandis here yet again with a small but at the same time BIG change for the “Pokemon: Best Wishes!” anime! Our once badass as heck villians now...