Well, for me, I plan out everything, like, who's the antagonist, what is the character of the rival(s), and what is the plot of the antagonists...
First, the antagonist, what is their goal? I'll fit that to the storyline...
Like my hack...
Pokemon SkyWhite,
The plot is:
In the region of Sky, the military forces is preparing, why? The other region, Viros, is planning to conquer Sky, Rust, the Governor of the Region Viros, said that they must expand their country, as the President, Dark stated. But do they planned that plan alone? A horrible idea crept to Dark's mind-they should make the world clean by clearing Pokemon from the face of the Earth starting with Viros to Sky, making the world "good."
While they are planning this, White/Pink ,from Sky, rose to be a trainer, wishing to succeed with the Gym Leaders and the Elite Four, and the Champion alike, while kicking the butts of Team Conquer, the team Dark created to conquer Sky.
Ignore some grammar mistakes....
I'll shape out the antagonists by the plot...
The antagonist's goals is to conquer Sky...
Which fits the storyline...
Maybe I got a bit off topic....xD