Not everyone wants to smudge/scratch their screens, and fingers still work on resistive screens. Yes, there's a greater need to maintain pressure, but it still works.
Inconvenient? Perhaps, but then there's the issue of accuracy. Not only technological (for which capacitive is inferior), but also ergonomical. I might agree with your point if we were talking about a full-size monitor. But a controller's screen is going to be relatively small, even if not as small as a DS's. Take it from someone who prefers to leave their stylus tucked away safely: fingers simply do not provide the level of accuracy that you will often need on such a small scale. And sure as hell not MY fingers (ask PB).
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.
Actually, it is EXCEPTIONALLY difficult, given that you're talking about a system that's already out. Even Nintendo lacks the ability to time-travel; what you're suggesting would be impossible without cutting off older projects, thus fragmenting the userbase. Even if that is overcome, backwards compatability is a pretty major point of most Nintendo handhelds and is especially so with the 3DS (given that they're opening it up to DSiWare and never-before-done-by-Nintendo system transfers; they'd have to rework the e-Shop to detect and accommodate the specific 3DS model, and nobody's going to like taking their latest piece of hardware online to find out that their hardware forbids them access to certain online content).
It's generally not good press for compatibility to vary by the individual SKU, as Sony learned (we hope) the hard way with the PS3.
Even assuming for the sake of argument that Nintendo is going to use a capacitive screen, it would be CONSIDERABLY easier to "program twice" for the Cafe, which is not yet in the public's hands, than for the 3DS, which already is. Further the Cafe has no backwards compatibility issues with regards to touch sensitivity; no Wii game uses it.
tl;dr
Your premise is questionable, but at least possible. Your work-around is completely illogical.
Also on DeviantArt, Rumble, DLive.tv, and the Fediverse (@freespeechextremist.com and @bae.st)