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.
The game runs at 30 FPS instead of the N64's 15~20 FPS, and much of the assets were re-done with a higher resolution. There are other changes like the Bomber's Notebook that someone already mentioned, which makes it easier to keep track of which heart pieces you've already attained. I think it's a fantastic remake.