If I had to make a platform with physical media, I would distribute games on SD cards.

Games would come on a micro-SD card, coming inside the box inserted inside a full-size SD adapter for compatibility’s sake.

The boxes would probably be around 3DS box sized to enable including a manual, proper box art and a back cover, while being compact.

I know this is controversial but I would make the boxes out of cardboard. Collectors can keep them, and non-collectors can just throw them in the recycling.