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 redid the boss battles and there were other changes like the Bomber's Notebook (Which is overall good in the remake, but the constant notifications quickly started to annoy me). If you have the time, this video explains perfectly all the changes (And funnily enough, it's by the same guy who's making the HD textures):