If you could experience pokemon from a villain's point of view, how would the system work in terms of progressing through the game? Would you have to fight rival gang leaders in stead of gym leaders? That's what I was thinking. Would there still be an elite four? How would this work friends?

Maybe you could steal the badges from the gym leaders. They are all pushovers.

I am a friend!

BS is a friend to all pokemon criminal elements and an all around good guy

Yea I could see stealing badges as a form of progression through the game, possibly some elements such as turning a pokemon so they learn dark moves or something?

I think it wouldn't be much different than, say, N's journey. He defeated all the gym leaders and worked his way to his designated legendary, leading to his ultimate goal. I guess this isn't too much of a difference when compared to the actual game plot.

N's story would be pretty awesome, though I was thinking more on the side of being an organization member or something like that.

Maybe ranking up in the organization?

yea yea, so you could become like a head boss and gain access to more powerful pokemon or something.