While I'm still sorting out a lot of stuff, I have an idea I'd like to try. I don't know if I can do it, but here it goes:
Arceus, seeing the different ways humans have exploited pokemon and gone after his legendary kin, has decided the time has come to destroy the human race and start all over. However, Mew argues that for every bad human, there is a good one as well. That humanity needs a chance to prove themselves. Arceus decides to allow Mew the chance to chose a human she thinks is best.
This human is the player character. Here are my main goals for the hack:
1) To create a new region and bring in pokemon from all five generations. This would include a series of brand new characters.
2) Involve a series of challenges in addition to the gyms and elite - or maybe replace them all together.
3) Create a captivating and unique story line and game experience.
This will take quite a while to develop, and is still in it's barest stages... just sharing an idea here.