Like, i don't know, having slightly modified pokemons, whether it be through a mask, an aura, or anything, with perhaps different typing or exclusive moves/stats attached to them.

I know this is sort of reminescent of Pokemon Colosseum & Gale of Darkness, but i'd like to take it a step further and through less linear means than Shadow Pokemons: Keep the idea of a group of scientist toying with Pokemons, but make it actually matter in the most important scheme of things, which is battling