The 3DS version of Super Smash Bros. will, however, make use of the New 3DS's c-stick.
Early-adopters of Nintendo's circle pad pro accessory for the 3DS will be disappointed to discover that its upcoming Super Smash Bros. title will not make use of the device. In fact, on the official list of titles that support the circle pad pro, Smash Bros. is the only one that specifically states that it won't support it. This is most likely because the game will, however, support the c-stick on the recently announced "New" 3DS.
It seems somewhat perplexing that the game would support the c-stick, but not the circle pad pro, which essentially perform the same function in the games that they are used in. A NeoGAF user points out that the circle pad pro obstructs the 3DS's infra-red sensor, which Super Smash Bros. will apparently use to interact with the new Amiibo figures.
The upcoming Super Smash Bros. title will be the first one on a Nintendo handheld. All the prior titles were on Nintendo's home console, and utilized the c-stick for quick smash attacks.