What gameplay changes did the make in MM3D?
Only thing I can think of is changing the swimming mechanic when a Zora. They improved it in all aspects, except going super fast drained magic unlike before.
They changed some bosses up, most notably Twinmold, and I also remember the bank in Clock Town being located in a different (and much easier to find) place. The boss changes were weird, though - they mostly just received huge eyeballs that pop out when they enter the "hit me" phase, which was really pointless, and then Twinmold, well, they changed the whole battle by making you get the giant mask only halfway through it.