Large file sizes aren't inherently tied to the amount of content in a game. Nintendo's games especially generally do not have very large file sizes (comparatively to other developers), but there's usually a lot of game in there. It depends on what developers are using that memory for.
The download and disc will likely be identical, outside of maybe Nintendo offering a special gift for going the eshop route like they're doing with the Donkey Kong Original Edition with select 3DS titles.