That's exactly my point. It can bring even more awareness to the franchise. Imagine kids getting it on their iPod touch and then asking mommy for the new version with all the latest bells and whistles which is only available on the 3DS. That results in much more than a 4.99 sale of a single game, for very little cost.
Basically it's great marketing for the franchises (and thus the 3DS itself).
To Nintendo that's a giant risk for them to take. What if they released Pokemon yellow on the iOS platform? Then they'll expect another one and another one and so and so on. All of this on the iOS platform. This will attract less people to the 3DS. "Whaf do I need a 3DS for? I can play these games on my iPod touch/iPhone/iPad."