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Eh, I don't really mind the whole Blue/Green debacle. He was brought here as Blue, so it'd be strange if they changed it, now. After all, it's a callback to the original games, and since it's a nostalgia call they can't go changing things, then fans that would be the subject of that nostalgia would be like "WTF?"
It's because of the series being a callback that they can't do it.
But the original games for us weren't Red and Green, they were Red and Blue. Similarly, the protagonist and rival for the games for us were Red and Blue, respectively. Wouldn't be appealing to our nostalgia if they called him Green.