Unless Capcom managed to compress the files so they could use a smaller card -- doubtful since this effort would only apply to the American release -- I'm sure their "weeks of effort" were simply a negotiation with Nintendo to reduce the manufacturing cost based on production size, marketing dollars, future cooperation, etc. Capcom probably assured they could meet the economy of scale that has so far only applied to Nintendo's first-party titles, so they argued they should get a deal on the card production price that is similar to what Nintendo pays for its own games. Given the quality and appeal of the game, Nintendo probably decided that taking a small hit on their own margins would be worth it in the long run.