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The whole reason the journey starts is to research the so-called "new" phenomena, Mega Evolution. A lot of people in the game haven't even heard of such a thing. Yet there's a giant Mega Lucario statue and tower in the middle of a town. The champion knows how to mega-evolve her Pokemon. The old man in the tower said he's the great-descendant of the very first person to use mega evolution?
Why did Korrina get more story involvement and screen time than Diantha? Who are we supposed to care more about?
How did Sycamore become a Pokemon Professor if he's so bad at battling?
Why did your rival use the same team of three Pokemon for the entire game until the post-game? Isn't he/she a very serious trainer?
Why did the legendary Pokemon that had the potential to destroy the world only blow over a few houses when it woke up? Kygore and Groudon had way more build-up to them.
Why did Lysandre broadcast his plans across the biggest source of information in the world? Wouldn't he want his plan to succeed?