I guess Majora's Mask was supposed to be benefit from the New 3DS, but I'm not sure that's the best sign for a system that it takes updated hardware to play an updated N64 game better lol
It totally isn't outputting a significantly higher polygon draw rate... an improved framerate... twice! because of the stereoscopic 3D. I mean it isn't N3DS exclusive either, it supports that c-stick. (you should keep that rendering twice thing in mind when thinking about Xenoblade Chronicles 3D).
Smash Bros. looks so much better than I was expecting (even on the standard 3DS, the screen size is about tolerable). Super solid framerate, though it does take a brief naptime to start up the game, as it's booting in own proprietary OS to free up some RAM of the 3DS features not being used.
If you wanna talk about bad performance on the system, Pokemon has got you covered. I simply haven't noticed any drops with Xenoblade yet. (for rreference: I'm at Bionis Leg, encountered a mechon that talks)