How MINE would work:
You start in the large city of Shelldo, known for its famous dream fountain. Each city has a guardian pokemon. As you and your parents leave the house, Team Sandbind kidnaps your parents, and burns down the pokemon center. For some odd reason, the guardian of Shelldo, Relicanth, did not awaken in such a time of need. It, was stolen. Every gaurdian pokemon has been stolen by team sandbind using a device called the Pact Sealer. After you save your parents, your rival informs you of the pokemon league. As you go through the game, you defeat gym leaders, soon after, you must battle that areas Sandbind base, and you must fight that towns guardian, slowly destroying the pact sealer. Defeating the pokemon leagues guardian pokemon destroys the pact sealer, causing the legandary of the game to be summoned, Stalitan (rock/ice) You may obtain each guardian after catching or defeating Stalitan.
The gameplay will also be completely different. You battle in a full enviroment, it is not turn based. You run around freely, changing move styles. Extremespeed would freezetime, and when you ran into him it hurt him. Shadow ball would should a large dark ball at the foe, causing a realistic knockback. Catching pokemon will be just as easy though. Weaken, status, ball. Wild pokemon will stay random encounters in tall grass, caves and water. Surfing will be the same, but flying will be different. You must go through a very short flying minigame where you may encounter a pokemon. You may skip it once youve broken the Pact Sealer after recieving HM02 fly.
Hope you like it!