Back in the day, carts provided any special function the system couldn't do on its own. The bulk is serious there. Right now we can fit the processing power of 200 SNES into a handheld 3DS. If I were nintendo I would just make some privative pinout to write-once eMMc/MMc chips. Nothing fancy. (Perhaps the saves! don't forget the saves)
The system should be able to grab everything inside, and copy it to a place where it can run it, installing it or whatever it needs. After a install, putting the cart again in the system could be optional (probably not).
And filesystem matters. If nintendo still pushes FAT32 partition schemas into those carts, scalability could be a problem when carts reach over 128GB. They should look into a filesystem without journaling and scalability problems solved like ext2 or ext3 (No journal mode) or better yet something privative.