I also loved this game on the 3DS. I’ve recently been playing the N64 version as well, and I gotta say the 3DS version is so much better. I’m not sure what it is, but movement feels a lot less precise to me in the N64 version. I have some replays of me trying, and failing, to break a pot with my sword as adult link, like 8 times before finally hitting it.
Also, I finally understand why everyone hates the water temple. The iron boots aren’t an item in this version, so you have to go to the equipment menu every time you want to put them on/take them off.