They actually offered GBA games to customers who bought the first 3DS around its first week of release or so :U At this point though Nintendo's likely going to keep the rest in the Wii U virtual console. I'm guessing that's because since the 3DS gets new games at a much faster rate than the other, they think nobody's gonna pay attention to the older stuff on that system.
Plus, the GBA is very outdated at this point and I doubt newcomers would know what to do with a slot that'd be almost useless. This is why the DS dropped Game Boy support. Nintendo just filed a patent for an all-digital device as well so physical GBA support is dead.