Native creole, that means, creole as the only language for a wiki is the third alternative. It is suited for new software -- new wiki engines or other software that need a lightweight markup language. Existing wiki engines could offer administrators the choice with which markup to run new wikis. Wiki-Communities that are set up the first time (where no pages already exist) then could use creole as the native language.
Since the core WikiCreole is meant to be small and easy to learn, it will only reflect the common denominator of all wiki engine markups. Engine developers might want to extend it with more elements from their native markup (gradual alignment). Creole Additions is meant to help engine developers, that would also like to talk about a unification of those extended elements.