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For the Gen 4 remake.
I'd like one where you start as a former member of the now disbanded Team Galactic, one who truly believed what Cyrus said. After Team Galactic disbanded MC decided to start a journey (so we have a reason to fight gym leaders).
As he goes along the journey MC starts regrouping former Team Galactic members and sort of becomes the new leader, but this time TG is underground and no one knows it re-formed.
After proving himself to be the strongest by beating the Elite 4, he finally activates his plan, but near the completion of it, the MC from Gen 4, now much older with different clothing (but still recognizable) comes to stop you.
In the end Team Galactic disbands once again, and you end up getting a speech from Gen 4's MC and change your mind about following Cyrus' steps.
I don't know. I mean I want a game where you are the bad guys, but since we can't have the bad guys win, in the end you become a good guy.
Customization should be in game, so that your initial clothing is Team Galactic Grunt clothes, then change into casual, and as the game progresses you even get a Suit (Team Galactic Boss Suit).
Starters would be a Houndour, and game starts in an abandoned Team Galactic facility where Zubat/Croagunk/Bronzor/Glameow/Wurmple can be caught (Since those are Team Galactic Grunts' abandoned Pokemon).