Is this the first case of a game having the system's controller as part of the box art (not just in the corner or being part of the standard box design)?

This doesn't have to do with boxart, exactly, but what about Pokemon?

You're playing the game, wandering around this huge world where trainers see you and challenge you to pokemon fights, where pokemon attack you randomly in tall grass, where people don't play pokemon such much as a they live it. You walk into a pokemon center, and there are two kids standing next to eachother, holding gameboys, a link cable between them, discussing how they're trading with eachother.

That one sprite marred what was otherwise a completely cohesive world.

No, see, those were pokedexes.