Using X/Y graphics on 3DS. Spin-off game where you actually accept Team Rocket's invitation after the Nugget Bridge.

Immediately after accepting, your outfit changes to a Team Rocket uniform and you are given a training partner. After training with your partner through a series of pokemon battles and situational puzzles within pokemon battles, you get your first mission: Stop the title character from passing the Dig house in Cerulean.

Each mission you face the title character. If you win, you earn rank (and earn money) within Team Rocket. Although after each win, the title character's team levels up and gets stronger. When you lose, you lose rank (and lots of money) and you are forced to relinquish your highest ranked Pokemon to Giovanni. You can grind and capture as many pokemon as you can but your pokemon's levels are capped based on how many missions you've completed. You also gain rank by capturing or evolving rare pokemon and giving them up. You can also keep on going for badges at gyms yourself to increase rank and use HMs like normal. A mission is complete when you defeat the title character three battles in a row.

Missions:

First Mission! No Dig For You!

Stay Grounded Kid! Hold the Lift Key!

Protect the Tower! We Have Mr. Fuji!

Protect the Boss! Silph Co. Invaded!

Cycling Road Barricade!

Team Rocket Safari Zone Takeover! (capture 10 different pokemon to complete)

Surf Route Barricade!

Cinnabar Island Lockdown! Pokemon Mansion Secret Key Keeper!

Fiery Team! Assist Former Executive Blaine! (double battle at Cinnabar Gym with Blaine as teammate)

Power Plant Peril, Catch Zapdos! (battle main character for right to obtain Zapdos)

Seafoam Island Strife, Catch Articuno! (battle main character for right to obtain Articuno)

Viridian Gym in Sight! Help Boss!

Victory Road Vexation, Catch Moltres! (battle main character for right to obtain Moltres)

Challenge the New Champion! (battle main character after they have just became new champion)

Post-Game (with all 8 badges and defeated new Champion)

Boss Retiring? New Viridian Gym Leader! - you become the new Viridian Gym leader but you don't stay in the building, you get to roam like normal. Every so often you receive a ping that a challenger wants to battle you. If you decline, you lose serious money and you lose prestige (which was your former Team Rocket rank). If you lose too much prestige, you are fired as gym leader and must earn it back. If you accept, you automatically transport to the gym and battle. If you win, you win money, earn prestige, and increase the number of Earth Badges in inventory. You can also lose your leader status if you run out of Earth Badges.

There's also a Battle Frontier/Maison/whatever to battle at like normal newer games. Basically it would keep the other things like waking up Snorlax, Unknown Dungeon, and stuff.

Wouldn't this be a fun game?