It would be somewhat based around the Team Rocket Challenge (linked below), but with an actual story and stuff.
Features would include:
-New starters! For example Zorua, Sneasel and Houndour.
-No badges. The ranking system would literally be a ranking system, going from Grunt to Scout and all the way to Admin.
-A partner in crime! Rather than the usual rival, you'd have a fellow Rocket who'd accasionally join you on missions and such.
-Missions! You'd travel around Unova stealing pokémon and robbing places, and generally screw things over for team Plasma.
-Story! It would be focused around two things; recapturing Mewtwo, and taking down Team Plasma.
-Stealing! You'd be able to steal a trainer's last pokémon, and send it to HQ for rewards.
-Gym leaders would appear every now and then, trying to stop you.
Now, I know nothing about ROMhacking, or if something like this would even be possible. But, it'd be great.
Team Rocket Challenge:
http://images4.wikia.nocookie.net/__cb20130507160118/fossilfighters/images/4/47/Team_Rocket_Challenge.jpg