I'd like to see something new and interesting, like an extremely corrupt government. There could be curfews for citizens, military police around every corner, and maybe bans on battles and limitations on Pokemon ownership. And then, in the midst of it all, you could be a member of a resistance group. Going with that idea, you would recieve your starter Pokemon from a stolen government package intercepted by said resistance group.
To make this even better, the government soldiers, who would serve as the "grunts" of the region, would have a wide variety of Pokemon as opposed to the usual Poison and Dark types that every single grunt ever owns. That would increase difficulty, and the concept of a corrupt government would make for a more interesting conflict than we've ever seen before.
Building off the idea, the government could have been given this extreme power due to the legendary Pokemon. Maybe the legendaries were awakened years ago, and went on a rampage, destroying towns and burning things. The government could have started off as a noble organization, taking control of the legendaries to protect the people from their wrath. While this protected the citizens of the region, maybe a corrupt leader went into power. This leader wouldn't be complete, utter "evil", but he could have taken the desire for order too far, maybe even using the legendary for his own purposes.
This idea could be really interesting, especially with the possibility of a different type of protagonist. Maybe the game could focus on the struggle between the government and the aforementioned resistance group. The protagonist could be a member of the resistance, and the "professor" of the region could be the leader of the resistance group.
Yeah, it would be amazing.
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But knowing Game Freak, the team will be something like "Team Dark Evilness" or "Team We Hate Friendship". They will have the usual cliched goal of taking over the world by awakening the legendary. And you, the protagonist, will be a 10-year old who wants to be friends with everyone. Together with your team of Pokemon best friends, you and your best friend rival will fight against the purely evil team with no redeeming qualities whatsoever and defeat them, showing that friendship is as strong as 5,000 atomic bombs.
Life sucks.