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One of those traditional 3D action platformers with various puzzles correlated to abilities you obtain as you progress.
You play as an amnesiac but eccentric Ditto who starts with a extremely limited set of transformations. New transformations are acquired along the main storyline, with a few utility transformations available as side material. Also, in secret/hidden area you would be able to somehow gain access to evolved forms of your transformations (ie. Pidgey is used for limited flight; the upgrade would allow you to change into Pidgeot instead, with less restrictive flight capabilities)
There would be boss fights as well, typically against giant Pokemon.
Still debating on whether transformation durations should be limited, or if the transformations would just have restrictions on their capabilities to compensate for an indefinite duration.
Haven't thought too much with regards to the overarching plot, but there'd be a cliche twist reveal at the end about how you aren't actually a Ditto, but a Mew unknowingly transformed into a Ditto
Alternatively, you could have a similar game with Smeargle as the star.