i already got some ideas for the game
cipher is the main villain and there will be shadow pokemon
halfway through through game the main characters discover that team rocket made an evil clone of red and gold (similar to evil wes at the end of coliseum) but they had their own ideas so they reformed cipher.
the world champion is NOT the final boss, because evil red and evil gold appear as soon as you beat the world champion and a final double battle begins (they have 12 pokemon as they each have a full party)
evil gold has 6 shadow pokemon:
meanwhile evil red also has 6 shadow pokemon:
okay so after the double battle the evil doppelgangers open a portal to the distortion world to fulfill their master plan of turning the every pokemon into a shadow pokemon so they can recreate the world in their image. but then all the shadow pokemon the villains have sacrifice themselves to imprison the villains in the distortion world. but then the villains drag the real red and gold into the distortion world for a REAL final battle. the power of the fading pokeworld somehow revives red and gold's pokemon and ups them to level 200. and the distortion world gives the villains new and improved pokemon that are level 200. what pokemon the final bosses have is yet to be decided
if anyone has good ideas for story elements POST THEM!!!!!