I don't understand your premise, for two reasons:
1. By what logic would Nintendo employ a more expensive technology for their home console? If anything it's that much more detrimental seeings how controllers are a "peripheral" that ideally a gamer should be buying more than one of, and the screen/streaming tech alone will likely raise cost concerns.
2. Why exactly do you suggest that a capacitive touch screen could substitute for a resistive touch screen, but not vice-versa?
There is the problem of how each works and the accuracy and ease of either.
The resistive is what DS uses and the 3DS almost needs to use one due to the accuracy needed by the resistive touch screen.
Given the chance to use either for a controller, capacitive is best due to the ease of use. You can use your finger and you can maintain contact, while moving, a lot easier.
If Nintendo wants to try to use the 3DS as it is now for a controller, they will run into the problems the resistive touch screen has.
If a consumer is willing to forgo complete NDS touch screen "sameness", they can get a 3DS with a capacitive touch and that would work as a controller for the Cafe, but then all the games for 3DS that use and expect the resistive screen would have to be programmed twice for either method. It wouldn't be that hard though.
tl;dr
The only reason 3DS has Resistive Touch is for compatibility with NDS games. Given the chance to use either, Capacitive Touch has way too many more advantages for use as a controller.
PS: I can go into detail on any part I may have overlooked, just specify.