I always wanted to see a Rock/Paper/Scissors legendary trio, with an Origami legendary with Protean ability to tie them all together.
The subplot would be all about how pokemon types came to be supereffective against each other, and how, say, a fish pokemon is imbued with water "power" and certain water properties, instead of just being a fish.
So basically, have Gamefreak answer the age-old question: what makes a pokemon a pokemon?
The only problem is that I can't think of a good legendary for the Paper one, since it would have to be weak to Steel and supereffective to Rock.