I like the idea of doing something with the starter pokemon. Maybe something along the lines of having an NPC in the Grand Hall who will teach moves to the weaker starters at various stages. Taking chikorita as an example, maybe let it get leech seed after the second gym or in case of squirtle let it get rain dance, so that it's ability becomes useful. Though I don't really use weather teams so I can't say how it would effect the game specially with so many different fields in play.
Another thing that came to mind was adding non Canon starters? Maybe based on different types. There could be a machine or something in the room with the starters and you can enter the type you want to use. Then the machine gives you the option of a pokemon of that type. So if somebody wants to use a rock starter then they get a geodude or something. Maybe an elekid or tynamo or something for electric. Just giving the idea out there. The pokemon can be anything.
Maybe we can also give certain items only for specific starters. So while Torchic doesn't get anything, a starter that isn't used too often could get a held item like a choice item or orb. That would be a really big incentive to use that starter.