This actually sounds like a great idea, I wanted to do something like this but I felt nobody in fan editing really cared about Pokemon so I probably shouldn't bother. These are ideas I'm going to give to you for your fan edit, I might help you out if there is some trouble you have or anything.
1. Add the deleted opening about the lost daughter of the scientist, you can find it on the Mewtwo Returns DVD.
2. Replace all the music with the Japanese music except for Mewtwos theme in which the american theme is MILES BETTER.
3. Edit it more in tone with the Japanese version whilst retaining the american dubs (You may have to re dub some lines)
4. Remove Mewtwo destroying the lab and instead only destroys Giovannis lab (It basically repeats itself twice)
5. Tell the story of the Japanese version where the story is much more complex.
6. Significantly reduce Ashs role, its Mewtwos story.