I actually have a story of how two of the changes collided to make a really annoying experience. When heading back to the pirates fortress for the stone mask, the new swimming cause me to lose all my magic meter, so then when I got to Shiro I couldn't give him a red potion (no magic = no lens of truth) so I had to warp out of there for some green potion first. (And while we're on the swimming, 8 minutes straight of holding A and R for the beaver race gave me a huge hand cramp!)
As much as I dislike a lot of the changes (the only ones I like without question are the graphics, the touch-based item inventory, gyro aiming, new Gorman quest and the song of double time), this was the first time that I really got to get into what MM is all about. Without using any guides and only having a faint memory from 15 years ago of how the game is played, I managed to 100% the game (had never done before) without even using the inverted song of time (which I always used in the original). It was really great and rewarding, and it let me fully appreciate the dungeon design (there are so many short cuts when you start them on a new cycle with the dungeon item).
While I would have preferred an OOT3D style faithful remake that just focuses on ironing out the slight issues with the original (ie. how useless the old song of double time is), MM3D has been one of my favourite games in a long time.
PS: By the way, does anyone know if there is a way to play with the inventory handling like OOT3D? In OOT you just needed to tap on the item, then tap on the touch-button you want it assigned to (meaning you could easily use your left thumb to tap an item, then tap the touch-button with your right. All without repositioning your hand). Now it seems you need to slide it across the screen, which (on the XL models at any rate) practically requires that you completely readjust your hand position.