Yeah Wii looks better on that comparison. Even that version had fps issues, though they were excusable given how good the game is. I expect the 3DS version to be optimised to Wii quality at least. If its worse, i imagine that the areas where the Wii slows down the fps will go down to 1 on the new3DS.
Either way i wont even consider getting it because i already got the Wii version, unless they add extra content to it.