So what you're saying is that a bit of a lose-lose kind of expectation should come about at first concerning the evil team, and after being at a disadvantage at first, we train and get stronger, and then kick-ass? I like this. XD
(bah I meant to reply to you earlier D=) Well, yeah. Maybe like this:
At the start of the game, the thugs control the region, to an even greater degree than Team Rocket did in Kanto (and at the start of R/B they pretty much ran the entire business over there). The baddies are in power, you have to pay for safe passage, the gyms are shut down, the Elite Four have fled, and the Poké Centres are threatened by mafia takeover. Shortly after the start of the quest, you gain their attention, are noted for your power and eventually become cornered by a team of thugs who want to take your Pokémon for use by the (evil) mayor. That's when you encounter... la Résistance (the Elite Four being their leaders). Throughout the game, you and your companions chase the baddies from city to city. You manage to stop their evil plan to hack the PC system for personal use. The rightful mayors of the region are put back in charge. Finally, the evil team is defeated, their iron grip on the region released, and the Elite Four once again return to office. Having fought your way through the region, and challenged the gyms as they reopen, the Elite Four accept your challenge and give you a try at defeating them. In short, you are the "evil" team, and have to fight the established status quo, changing the region to your preferences.
Well, that's probably not going to happen, as portrayals of a corrupt government aren't entirely uncontroversial. It's definitely safer to go for an evil, one-dimensional team who are up to no good and who doubtlessly are the bad guys. Still, I would love for the Elite Four to be a little more active in the story line, instead of being anonymous faces standing in their rooms in that huge building in the middle of nowhere.
Like I said before, I'd be nice to have modest villains. Team Rocket believed in a gradual takeover, by sneaky methods. They wanted to rule the world, sure, but they didn't want to march on the capital and overthrow society through a direct confrontation. They simply wanted to gain more and more power until they one day owned it all. At one point, they had total control of the strongest Pokémon in the world, and used it to their advantage, but it was all done in quiet. No flooding the land or evaporating the sea, no ominous clouds springing out from a mountain peak or even any freezing of a city. Mewtwo worked - and escaped - without anybody taking notice. But since Gen. III, it has always been about using legendaries to force their way to the top, often with the risk/threat to destroy the world. It's time to put less at stake again, having meaner but less direct criminals.