If there are any in a player's sideboard, those are removed as well
Outside of Grass decks, Grip and Squeeze will almost never get used (In fact, I don't think anyone has ever used that attack in the Cube)
The main differences to pay attention to with Light/Dark Pokmon is the aesthetic (Light Pokmon cards feature serene, heavenly art and Dark cards feature the opposite) and their attacks
Place the enlightened counter on the indestructible Avacyn, Angel of Hope so its more difficult to remove, or pop it onto a changeling land like Mutavault, where it'll keep you safe as long as the land sits in play
The only saving grace for your opponents is that they don't buff themselves, but you'll figure out a way around that easily, I have faith in you