The Nintendo 3DS, like most Nintendo systems, had the hardware for several generations of older systems in it. It had the full GBA hardware, and it could fully play almost all GBA titles. Nintendo gave away a few GBA titles as a "super secret squirrel fan club" promotion, but never sold any on the 3DS. They threw away a lot of possible game sales, but why?
They'll never say, but the most obvious failing is that the 3DS could not sleep while a GBA game was active. You can close your bivalve console, and instead of it going to sleep the game just keeps on going. That was an unacceptably inconsistent and bad experience for a kid-friendly console.
Nintendo, who controls the firmware, the OS, who validates every game, WHO DESIGNED OR SPEC'D EVERY SINGLE CHIP IN THEIR BOM, simply could not figure out sleep. And they lost a medium-sized fortune in BC game sales over that.
Maybe sleep is just a hard problem?