Hey bro hope your open for some suggestions because this game is rocking rocket..
Some Suggestions:
1.) Since you cannot fight Gym leaders for badges and enter the Pokemon league then have like 8 PROMOTIONS and create a first ever "ROCKET LEAGUE" where you battle 4 superior-commanders before battling Giovanni. Wait wait..this is the best part.. After beating Giovanni you get Promoted and given a mission which leads to an event of battling the Elite Four!!
2.)Okay you know that event in Fire Red where you battle TR in Silph Corp? well there were a group of 4 TR members called the "BROTHERS" and they were stronger than the rest of the grunts. Could you make this one of your PROMOTIONS.
3.)Okay now since Team Rockets are Poke - Poachers. what about getting pokemon as rewards for completing certain missions. As you get Promoted you also get rewarded a stronger Pokemon depending on Your Promotion. Since the pokemon would be at a low lvl when you recieve it, this is where you decide whether you want to train that pokemon or catch your own, better yet "STEAL" your own.
Just some suggestions or requests that pooped in my head..but its all "What IF'S"
1) Wow, what a new idea. And while we're at it, why don't we make it so that each of the 8 promotions is a battle with a Rocket Executive who uses only one Pokémon type? And there's one executive in each major city? That way, ToxicPurple will be exactly like every other Pokémon game out there!
Sorry for the sarcasm, but I made it so that you "cannot fight Gym leaders for badges and enter the Pokemon league" for a reason: criminals don't do that stuff. (That, and I'm a little bored of seeing the same generic cliche canon-ripped plotline in every hack.) Why would Team Rocket structure their organization to imitate the Pokémon League, including exactly eight promotions followed by a battle against four elites and then with the head honcho?
For one thing, that would encourage Rockets to try to defeat and replace Giovanni, and he would be an idiot if he actually encouraged his own (lawless, brutal, greedy) underlings to try to defeat him. It'd be especially dumb for him to then promote a Rocket that BEAT him in battle. That is a hostile takeover waiting to happen, and Giovanni's smarter than to willingly let things reach that point, much less encourage it.
For another, why would they make a "Rocket League"? The original Pokémon League is basically nothing more than a sports league, sort of a crossover between boxing and dog fighting. Team Rocket is not a sports team: they are in the business of MAKING MONEY, and lots of it. It'd be a waste of time and resources to set up what was basically a sports competition in between their employees. Sure, you'd prove that your Pokémon team is stronger than Admin Bob's, but if Admin Bob is running a huge smuggling operation between six cities and all you've done is battle wild Pokémon to train your team, you're a worthless Rocket.
There could be good reasons for a Rocket to battle the original Elite Four. However, if the reason they're battling the Elite Four is simply to battle the Elite Four, then that's a worthless objective. You will battle at least one Elite Four member during ToxicPurple, but it won't be simply to win the battle: it will be to further Team Rocket's objectives of stealing lots of Pokémon and making lots of money.
In short: Team Rocket is organized like a criminal organization, and your promotion through the ranks and progression through the game will thus be organized in the same way. There aren't eight set promotion levels in Team Rocket (or even just eight promotions in the game): with the exception of the first promotion (which is just to show the admins that you've got potential), you get promoted when you do things that impress your superiors and that are useful for Team Rocket.
2) Yep, the four brothers will be referenced. You'll meet them at least once. Their names are Shinobu, Shigeo, Hideki, and Satoru. If you can figure out the significance of the names I'll be impressed. No, you don't get a promotion from them. Why would they give you a promotion? They're stronger than the average grunt, but that and their interesting family is all that differentiates them from other grunts. They're the same rank as you.
3) That's already planned: you'll get rewarded with Pokémon for SOME missions. Not all, though. Not every mission you go on will earn you a promotion, not every promotion you earn will be due to the same type of mission, and the rewards that you DO get for various missions will also vary: sometimes cash, sometimes Pokémon, sometimes items, sometimes an opportunity to go on another related mission, sometimes nothing more than a pat on the back. You do not get a Pokémon every time you get a promotion, or a promotion every time you get a Pokémon. When you DO get Pokémon, it will be for good reasons: not something random and unassociated like "Oh, thanks for disabling the Electric-run security system in Vermilion City, have a Scyther," but something logical like "Good job on smuggling that shipment of fifty Abra into the Celadon Game Corner, go ahead and keep one as your reward."