>>55192837The most important thing is objective
Giovanni was a mob boss, pretty clear and realistic motivation
Ghetsis wanted to use political extremism to become a dictator. Dark but realistic, very cool
Fucking team magma and team aqua wanting to destroy the environment for no real reason doesn't cut it now like it did 20 years ago. Team star being just a bunch of bullied kids isn't cute, it was retarded and the worst part of the game.
Once you establish a goal, you think what the villains steps to get to his goal are, and how the hero stopping some of them causes them to react (the villain reacting to the player and changing in plans GREATLY improves the storyline). Trough this simple action and consequence reasoning you will quickly find how the storyline writes itself smoothly. At leats this is how I do it in DnD.
Finally once all of this is done, according to what came out of it, we can find an according aestethic, so a name for the team, what pokemons they might use, how they dress, etc.
I know this post is virtually useless because I haven't actually written a team, just set some rules for it, but I think these rules are important to set before you write a story for a piece of media like a game.
Also
>>55193524 is kinda cool, though I would propose an alien pokemon is the cause instead of a virus, much easier to write for because it doesn't have bigger implications on the world, while a virus pokemon is gamechanging for the lore.