So, which of these ended up the best?
Star Fox 64 3D
Ocarina of Time 3D
Majora's Mask 3D
My pick for top I think goes to OoT, with Star Fox following. Both play as you remember it and have aged well for newer players. True, some lament the lack of online in the latter, but it wasn't that great of a multiplayer mode to begin with so... eh.
The worst I think is Majora's Mask 3D. The game suffered from "George Lucas Revisionism" and the boss fights above are evidence of it. So few changes (like the save system) were for the better, the majority ended up being for the worst.