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I would've liked it if Iris had Trip's ambition to defeat Alder and become the champion herself in order to prove that she can do better then a Gym Leader. Oh, to make a reference to Ash and Gary, Iris and Benga could be rivals.
Cilan could've been the youngest of the gym leader triplets, trying to improve himself and facing his fears in order to become a real gym leader.
Dawn's appearance in Best Wishes sucked. She should've interacted with Ash more. Why wasn't a Wallace cup organized in Unova? I know Unova doesn't have contests but that could be pretty cool if Ash and friends entered as well.
Brock should've atleast appeared as well, not counting the Cilan special. What about an arc? Well - he could catch a Audino I suppose or cure a legendary Pokemon.
The Team Plasma arc could've been a prequel. Like the Legend of Thunder, but a 4 parter that showcases the journey of Hilda/Hilbert, Cheren and Bianca. And after that? The B2W2 story line could've started.
Team Rocket was simply shit and I don't have a fucking clue what to do with them.