Kuwahara says that the unnamed, would-be Game Boy Color successor was in development in 1995/96 and based on a 32-bit ARM RISC processor. The system, which evidently stalled in development due to poor graphics performance, is most likely the fabled Nintendo "Atlantis" project.
The second, more recently scuttled R&D project was basically a Game Boy Advance SP with a touch-screen fitted over its flip-up display. The unit's innards, as Kuwahara explained, were actually from a Game Boy Color. With a deep, serious tone in his voice he recounted that it "was not well received" by Nintendo management. The reason? It wasn't backlit (being GBC tech) and the touch overlay made it even darker. Shigeru Miyamoto evidently liked the general concept, though; Kuwahara says he likes to think his ill-received creation influenced the eventual development of Nintendo DS. You can see it after the break.