Apparantly OOT 3D ran at about 30fps ( with occasional dips), and the original on 64 ran at around 20fps. Iwould expect MM 3D to run the same as OOT 3D. I do not expect major differences between playing on the New 3DS and the regular, especially not higher res textures as someone mentioned. I think the extra ram is used to be able to open the improved internet browser/Miiverse while the game is suspended. This is already impossible with both Smash bros, and the new Monster Hunter 4 demo on regular 3DS.
Eventually I think we might get games with bigger differences.. but to be honest I think they wil either turn into NEW 3DS exclusives like Xenoblade, or maybe 2 versions of the same game. I just hope the next Pokemon will have a stable framerate in 3D, and preferrably the entire game will have it enabled. Nintendo just doesn't seem like the kind of publisher to cut corners and release games/versions inferior to others.
Keep in mind everything is speculation until we test it though.
The more interesting question is: What has changed from the original?
I read somewhere about the addition of 2 Fishing ponds. And the new version seems use a more saturated color palette.
But what about new game modes? Majora's Mask MasterQuest or Hero mode? One can only hope. . .