We know that eShop downloads are far larger than the meagre 40MB allowed on WiiWare or DSiWare's paltry 16MB limit, but Team Meat's Tommy Refenes has told Nintendo Gamer (via Nintendo Everything) the 3DS's digital download limit is a very healthy 2GB.
Looking back at the restrictive file size limit that prevented Super Meat Boy from making it to WiiWare, Refenes said:
[WiiWare's] 40MB is horrible, but [3DS's] 2GB is reasonable. 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.
Of course 3DS comes with a 2GB SD card right out of the box whereas Wii and DSi both have comparatively little built-in memory, but it's not necessarily in developers' interest to fill that 2GB all in one go.
Recently Nintendo revealed it was considering full retail downloads on 3DS and Wii U.