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First off overhaul the stats, types, and move sets on all pokemon in an attempt to rebalance the game in a way as most people can play what pokemon they want over what pokemon will win.
After this we make Pokemon Dusk and Pokemon Dawn a remake of the first two games but vastly restructured. Pokemon Dawn is a more lighthearted game where the trainer starts out in Pallet Town in the Kanto. Trainer follows normal game path. Dusk follows basically the rival from Johto and is a darker game. They both crossover and meet. Only the first third of the games follow the gym2gym elite4 structure after which the game expands into and all over the two regions.
Story structure follows a combo of Zelda and final fantasy story telling.
New gameplay elements would include pokemon team building (stats the effect whole team), tag team moves (attack and switch with a pokemon who has a tag move), an eveelution for all types, no more new Pokemon ever, a mega for all pokemon, completly rework the way mega works, and a drop in drop out co-op in main game, also towns and cities would have new structuring and allow for free roam multiplayer options (allow people to join an online instance with real people run around the city.), and an unlockable option to start with any basic minimum 3 chain pokemon.
Sequel to Dawn/Dusk Day/Night same story but day follows a gym leader from Johto and Dusk follows a team rocket grunt from Kanto.
Plot wise you have 4 games that tell the same story of rise and fall of team rocket from 4 different points of view. it would be close to flow and tone to the manga. But would most defiantly involve corrupt gym leaders and elite 4 terrorist/dictators.
Sorry was in my iPad. Hope this isn't too dumb, I. High as fuuuuuuck...
