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I believe the difference in outfit is meant to denote that Misty isn't traveling in the capacity of being the water gym leader but rather a regular trainer, hence the normal non-themed clothing. Likewise Brock isn't showing off his ROCK HARD bod everywhere and is dressed more like he's going camping innawoods. Misty has even more excuse in her anime design as she ain't a gym leader yet, despite taking it more seriously than her sisters do. Plus she's got water themed costumes like the mermaid thing, the goldeen dress, swimsuits, etc.
