I just finished playing Pokemon Rijon Adventures and I was thinking about what I would like in a Pokemon hack. It occurred to me that Team Rocket has always had power in every game they appear in, but they are usually shut down before the end.
I thought that the Rival should be similar to the one from G/S/C. For those who don't know, that Rival was a thief who stole his first Pokemon from the professor shortly after you chose a Pokemon. I was thinking Giovanni should be beaten at some point, but he escapes. The Pokemon League was quickly overthrown by Team Rocket after Giovanni leaves. The Elite Four should consist of three powerful, but corrupt trainers and Giovanni. Maybe give the trainers some fancy name that marks them as Giovanni's top 3 officers.
When the time comes to fight a Champion, you fight against your Rival. When you win, your Pokemon are somehow healed and the police arrive outside. At that point, Team Rocket decides to make their final stand and you're forced to fight double battles alongside some of the officers. After beating a few trainers, the police Pokemon are too weak to continue, but they have enough medicine to heal your Pokemon one more time. At that point, you have one final battle. A Double Battle against Giovanni and your Rival, who reveals himself as Giovanni's son. When you win that, they are finally arrested and you are given an award for helping the police and declared Champion and savior.

I like my plan. If you want to share your idea leave a post. I'm no hacker, I just like this idea because Team Rocket doesn't get much recognition, despite their obvious power. No one else has ever commanded Mewtwo. That must say something. ToxicPurple has potential, but it's too short and the hacker doesn't seem to be progressing.

I like your idea. I have been toying with the idea of a TR is awesome scenario. Now the overall plan is fine but you only gave details on the ending. What about the badges? What about legendaries? Should Giovanni have Mewtwo in his final team since he can "control" it?

Some ideas i'd incorporate is basically doing a reverse G/S/C time. Start off in Kanto, and after you beat the Double Battle and become savior, you timeskip to 3 years forward. And go continue the journey in Johto. And also Giovanni broke out a year ago but has been missing. He went to Johto to build up that empire. So now you can go beat him in Johto. But there isnt an E4 since you only need one

ignavusd :
I really just meant this thread for people who have their own ideas about what a new game should have. My story idea was meant more as the first post. If you think of a different, but good storyline feel free to share. That goes for anyone. If you want to build on the stories of others, that's good too. Just mention who your building on.

Your post is good, I just don't want anyone else to be confused. This is open to any and all ideas, with or without a basis.

It would be nice if we can customize our own character and make our own starter pokemon(and evolutions) to play the game with. The stats would be the same as the normal starters except we put our own flavor to it.

I would like to include time from Gold/Silver/Crystal. It would be nice to see that.