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Zinnia is legitimately a fantastic character. She's an odd melting pot of various traits that seem cobbled together, yes, but each of those traits has an easily explainable root to it.
Her ultimate goal seemed reckless and shortsighted in hindsight, but that's because the only people who had mega stones at the start of the game were Archie/Maxie, who she decided to try using their plan to further her own.She also didn't give them the idea for the plan, otherwise, Team Aqua/Magma wouldn't have existed in the Ruby/Sapphire/Emerald Universe.
And her actions in the Delta episode were largely some of the most genre savvy in the entire series, acting mostly on violence and doing what she wants by force. Her not telling anyone her plan was also a smart move because you try explaining to scientists that their tested equipment will just send the meteorite to an alternate universe, and you should instead use your religion's way of doing it. They obviously would have used the Link Cable in spite of her warnings, because she sounds like a loony.
She also 100% deserves to be in a new pokemon game If only to make /vp/ absolutely livid.