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Lillie isn't a bad character and she's not a mary-sue, her execution is just fucking terrible. From the start of the game, she steals the show from you. She openly, blatantly commits theft of the spotlight because she's so "important" and her story "matters", while you get zero input into the decisions the game makes for you. This removes player agency and the concept that the decisions and actions you take matter.
I'll probably get hate for this because
>gen 5
but lets compare Lillie to another female "side" character, Bianca. Now, Lillie doesn't have to be Bianca. They're different characters, but their plights are similar. Bianca's not the greatest at anything, in fact she's pretty damn bad. But Bianca's biggest character point is that she tries. She wants to be better, so she DOESN'T have to rely on you or Cheren. This is good, it means she wants to develop as her own person and character independent of you. Lillie does not. She spends the whole game fawning over how awesome you are while you effortlessly brush away all of the issues that are plaguing her.
This is the core problem: you're not the main character, Lillie is. The game isn't about YOUR development, it's about Lillie's as a direct response to your intervention. If she had shown up about half as much as she did, that would have been one thing. If the story had been about you just going about your trials and she was off doing her own thing until you happen to run into each other again, that would be another. But the story doesn't care about you, yeah, woo, cool, you're a good trainer. Whatever. HERE, LOOK AT LILLIE AGAIN, AREN'T HER PROBLEMS ENDEARING? WHAT DO YOU MEAN YOU DON'T WANT HER TO DRAG/FOLLOW YOU AROUND SO YOU CAN DO EVERYTHING FOR HER BEFORE SHE RUNS OFF TO KANTO WITHOUT GIVING ANYONE CLOSURE?
It's not about the character, it's about how much GameFreak tries to cram her down your throat, while your character just smiles their blank smile and asks for more.