The main problem many people discuss when saying is that the 3DS cartridges don't hold that much data. I'm not sure on the cap of what the amount of Gigabytes a 3DS cartridge can carry, if they can even hold a Gig, but if they really want to make the maximum amount of characters as they can while making a reasonably sized roster, they should actually take a page out of the Vita's book. Yes, the Vita is a terrible handheld, but what I'm regarding is that instead of having a spot on the cartridge to hold save data and take up space, all saving should be done on an SD card.
It would make sense, as you can have all the content itself on the cartridge and the save data in the SD card, but if that's not the case, imagine how much space saving all the data would take up. For my example, I say take a look at Brawl's save data on a Wii machine, your average Wii game's data is small, around 1-2 blocks. Brawl's save data takes up a whopping 48 or more blocks, which is huge. This will also be a problem for the 3DS' roster as the things that take up the most save spaces are the characters themselves and the overall trophy/sticker data in the game. However, since there's no more real story in Smash 4, Stickers may not have a purpose to come back, which saves some space. I'm still concerned though, and I know I'm not the only one who sees this.
Edit: Looking at my own WIi, I was way off. Brawl's save data takes up a whopping 128 blocks, almost 3 times as big as I first thought. This makes me worry even more.