Unless Gamestop gets rid of another system by moving it into the Legacy titles, not likely. Most of the Gamestop I've seen aren't terribly big, all becoming very cramped because of the plethora of games, gaming merch, and gaming accessories they sell. Skylanders typically takes up a small portion of the store, followed by Disney Infinity with a similar sized zone. Amiibo takes up a smaller location at the moment, probably near the Wii U games. Then you have the different games and accessories lined against the wall. Probably a cutout full of Pokemon related merch, along similar video game items. Then a gift card center or two. Used DS/3DS games. Game demo stations. The counter. Sometimes a structural column. Not sure about you, but it's feeling pretty cramped to me.
Personally working at a big name retailer, our video game section consists of three or four aisles that has to fit as many video game related stuff in there (minus stuffed toys/trading cards/etc). Essentially one side of the aisle is dominated by Disney Infinity/Skylanders and their little demo stations. On the other side, about 1/4th of he aisle is covered in Amiibo. The rest is Wii/Wii U titles/accessories. The other aisles I'm sure you can already figure out go in a similar order for the respective handhelds/consoles. Now if it was just the N3DS regular ITSELF, that would be no problem. Move some 2DS boxes around, space made. But people are probably going to want to purchase the fancy covers... Where would those go? Gotta get rid of valuable product space, but what product? Sure I guess you could try trimming an aisle and cramming in whatever, but then it makes it a little more difficult for people shopping for that specific product.
And honestly, after seeing how "well" Nintendo handles the Amiibo disasters, I'm not confident enough in them to keep stores stocked with covers people want. If they convince retailers to stock the 3DS, then congrats! But it would be easier done through their own storefront than spreading thin across all of NA.
