Aw maaan, not much love for Team Rocket going on here! I mean, sure, the idea is outlandish, and would probably never be done in any of the games, but think of the possibilities here!
Let's say your player character just falls in with the wrong crowd, right from the beginning?
You're told to steal your starter from Professor (insert tree here), and the other grunts grab the other leftover starters.
You catch Pokemon in the field as well as stealing occasionally from Bug Catchers or Youngsters, or other mainly defenseless trainers that can be thwarted by a level 11 Zubat.
Your boss becomes impressed with the work you have been doing, and promotes you.
However, while you are doing your work, a kid starts challenging Team Rocket, and questioning their ideals.
You defeat him and drive him off from whatever hideout Rocket are using these days, but you're left questioning if what you're doing is right.
Eventually your character might decide to leave Team Rocket, and follow this trainer to the Pokemon League, seeking bigger and better things.
The other Rocket Grunts that stole the other starters could become other rivals for your character.
And BANG, you've got a redemption story on your hands, reenforcing the difference between right and wrong, while STILL letting you try your hand at Rocket's dastardly work!
I mean... No, Game Freak would never make a game like this, and even if they did, no one would publish it... But still, I think the topic of this thread is an AWESOME idea. And not just because I have secretly dreamed of joining this group... Or dressed up like a grunt for a cosplay event... Or wear a Team Rocket shirt to work sometimes... Or anything like that...