as far as the shedinja i think it could be easily worked into the story so the player is properly akin to its ability and ways to defeat it. like said player meets Jasper, has to do some mission (double battles or something) through some scary ghost ridden place. He uses shedinja and tells you some story about it and so on.
level 60s in the 8th gym, sounds like an epic pokemon journey! haha
level 60s in the 8th gym, sounds like an epic pokemon journey! haha