If it was bundled with a digital pre-install, then it's better off with no game. Digital is worthless to me, personally. Can't even resell that. If it would be a download code, then whatever I guess. That's easy to sell, and neutral to me. If it was a physical copy, that would be a hassle for digital players to sell at a decent price.
Regardless of distribution method, bundling the game would make the Collector's Edition of MM kinda redundant. I think it's better to just let people choose how they'll buy the game, while giving them a chance to get the cool 3DS by itself.