Like most people here already said, I don't want them to change the game completely. They should keep the general graphical style but with some improvements (more detail, better polygons, more trees/caverns/rivers/hills etc. in Hyrule Field). The 3DS probably suppoprts more memory than the N64, so a bit more story explanation and some bonus content would be really nice (more cutscenes etc). Also I'd like to see a Light Temple instead of just being given the medallion. They should make it so that if you pull out the MS, you first have to beat the Light Temple before you're able to go to the overworld again. Also, make the Ice Cavern a real dungeon and after beating it, Zora's Domain will unfreeze and you get to know about Jabu-Jabu's whereabouts (I think that's a major plothole that should be fixed - I mean there is so much story telling and interaction with the Great Deku Tree and Darunia - and when they got to Jabu-Jabu, they ran out of memory or what?).
IMO they should not make the Water Temple easier. Just make it easier to switch boots, and maybe replace them with a Zora Suit or something that lets you swim like Zora Link in MM (I liked that a lot more than the "clumsy" iron bots). Instead of making the Water Temple easier they should make the other dungeons a bit harder and less linear (especially the Fire Temple). Generally have more enemies along the way, like in LttP (esp. in Hyrule Field).