Potential plot settings for games and fanfics

-Pals with Isaiah: As opposed to the traditional "protagonist is the messiah of the new badass legendary" plot, an alternative plot where you happen to be friend of the actual savior would be a good change.

This can't really work for a game plot as games, by nature, must ensure you can catch the legendary. So, whatever savior role your friend plays should be temporary, either because she or he give their legendary to you a la N, or because they die off, leaving the legend for you.

-Knight of the Empire: Basically the primary plot of Final Fantasy games, this can work in Pokémon in various fashions, where Empire is either the region, the evil team, the league or international government.

This contrasts with the traditional "player is a newbie to region" as by nature the player(as in, the character they play as) would be aware of their working place.

-Loss of the starter: Starter Pokémon has historically been the closest ally of your trainer. This has only been used as an element in Black and White, however, when N talks with your starter. A bigger idea would be a "shooting the dog" trope used on the starter.