Because Super Smash Bros is a game that's at its very core, designed to be played with analog inputs. You don't let players play with D-Pads for the same reason you "forced" people to use the analog stick on Super Mario 64. Sure, some people complained that they couldn't use the option they were used to with the SNES, but truth is, when the game is designed to be played with a specific control option, that should be the control option available, as it'll simply be better in every way even if somebody has to get used to it.
But what happened with Brawl? Why did Brawl let us play with the D-Pad?
Because of the Wii Remote.
Not everyone has a nunchuk. Not everyone has a Classic Controller. Not everyone has a Gamecube Controller. They didn't want to leave those people out.
On the 3DS? Everyone has a circle pad. If every single player has the control option the game was designed around, I really don't see why they should let them use anything else when it's not going to meet the standards you want your game to have.