[@Sionnie] Already gonna point out some flaws and stuff. Twinleaf Town is a town in the Sinnoh Region, New Bark Town is in Johto. As for Pokemon, I'll allow custom spawning just so it will be easier to self-plot characters (Just don't spawn in stupid overpowered stuff like Staraptor or Aggron or something early on, if ever. Never spawn Final Form Pokemon to catch.). You can also start out with one or two Pokemon on you besides your partner.

Lucario would not work for a Legendary Guardian, the only time it could have ever been considered one was during Lucario and the Mystery of Mew. Suicune and the other Legendary Beasts, I'm gonna say right now, will NOT be available for Legendary Guardians either. They are going to play a part in the plot, I'm not revealing what yet.

And, last but not least, keep in mind that this is based more off the Anime than the games, so try to lean towards more Anime Mechanics (Longer Pokemon Recovery Time, Longer travel time between towns, more realistic Pokemon Battles, etc...). If you have trouble, I would suggest a D-20 System or something similar.