think that Nintendo will indeed implement the 3DS as a limited controller. The only reason it couldn’t be a full controller is the lack of a second control stick, but we don’t even know the specifics about the controller; there could be no buttons at all or something for all we know.
But it would be VERY wise feature 3DS connectivity. Think of it; Controllers are going to be above $50, maybe even $60. Even when the economy recovers, not that many people are going to want to spend that much money on over 2 controllers. Being able to use a handheld that you already own would be extremely beneficial, and it could even drive sales up for people that are on the fence about buying the 3DS, but want to buy it for its controller capabilities.