I'd make a game for the Wii U that played like Pokemon Colosseum and XD control wise, but was like the GBA games gameplay wise. You'd start out in a sort of post-apocalyptic Kanto where, after an epic battle between Mew and the Legendary Birds who had been captured by Team Rocket in an attempt to obtain Mew's allegedly limitless power, which threw off the balance of nature and caused the resources to deplete, and the remainder falling under Rocket's control, meaning they're in charge of everything. You'd play as the son of a Rocket Admin who was misled by his father into thinking that they helped people, and witnesses Pokemon being horribly abused by by your father and his friends. You decide to dedicate your life to helping pokemon and getting revenge on Team Rocket, while also uncovering secrets of the corporations history and how years ago, a young boy was able to overthrow the entire organization with the help of his friends and his pokemon. Eventually you'd face off against your father, after defeating his henchmen and ruining the organization, with an epic and emotional dialog, leading to the final battle with this music playing in the background:
The game is focused, like the others, around you growing not only stronger as a trainer, but learning how to coexist with the wonderful world around you and create bonds with your pokemon. I think this would be a more compelling goal in general, you'd feel a deeper connection to the story and getting revenge on your dictator father (who has put out a giant warrant of food and supplies to whoever brings you in). He also sends out stronger admins and bosses to find you, and when they do, they become sort of like Gym leaders in that there is one admin per type, or it could just be 8 and the finals, not too sure at this point.
Anyways, the gameplay is sort of a refined 3D hybrid of Coliseum and the GBA games, you run around in full 3D environments and trainers like Coliseum, and there are random battles and tall grass like the GBA games, with a structure more based on them. No shadow pokemon or snagging here, just good old tall grass (although maybe, to fix the random battle issue, you have pokemon running around like in Dragon Quest 9 in the grass, where they're harder to see, but still legible, instead of random encounters?). The music would be epic and more akin to games like Deus Ex and Skyrim in scope, as opposed to the 16 bit tracks of old, not to be rude to the legends or anything, but I could go for some battling while listening to stuff like
this. (<-Link)
The controls would work great with the Wii U's tablet, the table would work for everything interface-wise, like the DS's touch screen, while you could watch the High def Pokemon battles on screen. You could be running around while rearranging your party and inventory. You could also go co op with your friends over WiFi and explore the world together. It'd take place in a massive remained Kanto from Red/Blue and FireRed/LeafGreen.
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