WiiWare games are only allowed to be up to 40MB in size, a limitation that has prevented many games from appearing on the service, notably Super Meat Boy, which struggled to fit under Nintendo's strict guidelines. The ceiling has been raised quite considerably for Nintendo's latest system, however. 3DS games are given fifty times the virtual real-estate, topping out at 2GB.
Super Meat Boy developer Tommy Refenes told Nintendo Gamer (via Nintendo Everything) that "Super Meat Boy would have been on WiiWare if we could have had just a few more megabytes of space - you can only compress stuff so much before you have to start cutting out huge parts of your game. Unfortunately, at that point, it just isn't worth the time."
In the interview, Refenes described WiiWare's 40MB limitation as "horrible," but called the 2GB afforded on the eShop "reasonable." Team Meat has been exploring a 3DS release for The Binding of Isaac, a game that would easily fit the 2GB limit.
Because most 3DS cartridges store up to 2GB, most 3DS titles will be able to be served as digital downloads, should Nintendo decide to make them available via the Nintendo Network.