THE WORLD HAS YET TO REALISE MY GENIUS!
You begin the game as a New Recruit of The Team. The Professor is the Head Scientist and the Evil Genius of The Team, and your first mission involves stealing 3 Rare Pokemon. This will of course be laughably easy, and you are rewarded by keeping one of them as your own. Your rival will be someone who was supposed to protect or recover the 3, and will manage to rescue one as The Professor escapes with the last one. Then the Other Gender Character (who will be your Partner at times in the story) gets that last one.
Your assignments will be relatively simple, such as catch or steal a certain Pokemon or item, or deliver an item somewhere. "Gym Leaders" will be targets that The Team needs removed, so you (as the most promising New Recruit) are sent to defeat them. The badge is taken as a reward, because it allows your HM moves to be used outside of battle and pass through certain gates.
You can take as long as you need to complete these missions, and can go train, capture, play minigames, and other stuff, because you are a Loose Cannon Who Doesn't Play By The Rules, But You Get Results.
In the end, you defeat The Elite 4, capture a Legendary Pokemon, and become a Commander of The Team, second only to the Leader. Your Partner, who has stolen or captured enough Pokemon to fill The Professor's Pokedex, captures the other Legendary Pokemon, becoming a Commander of equal rank to you. The Bad Guys Win.
Then comes the third game, in which you play a fresh-faced youth on his/her Journey To Become A Pokemon Master. Along the way, he/she Captures a Legendary Pokemon, Battles an Evil Team, and takes down their Leader and his two Commanders, aided by a Mysterious Stranger (the Rival) with past connections to the Evil Team's Commanders...
It isn't the plot to Pokemon Black, White and ???, but it would be an awesome series! A classic Villian Protagonist story, with the third version undoing everything you worked so hard for in the first game!