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One of the best ideas Pokemon's had that emphasizes the collection aspects and the "my personal pokemon friend" aspects. There should be multiple types of "shinies" of varying rarities, such as the different sizes of Pumpkaboo or the seasonal pokemon, for every pokemon. You don't have to do much work at all, just scale the model up/down and have your artist shop a few extra textures.
There could be sidequests to tie in the varieties could make things interesting. For example, you could have an obstacle that requires a heavy pokemon to pass, or a trainer willing to trade for a purple-colored pokemon. Or, you can use the flocking feature from Gen 2 for when a certain sized pokemon becomes common in a region. Or even an island like in the show where all of the pokemon are "super-sized." There's lots of obvious wasted potential here to make the pokemon experience personalized like it was marketed, but then again that's pokemon in general.
