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Could they be pulling what they did with Lysandre in the XY anime where his first appearance was Alain's ally/benefactor? There was also his friendly meeting with Steven, and the genuine concern he showed for Marron when she was put into a coma.
But then again, we already saw elements of Team Flare present. Here, there's nothing that suggests Lusamine is hiding the personality she had in the games. Her relationship with Lillie is much more different, and I don't know if it counts but Burnet is being portrayed here as her best friend and a key researcher at Aether.
