[3DS] The Legend of Zelda: Majora's Mask

Graphics(obviously)
Some people say some music tracks were changed
They overhauled the save system (permanent save)
They added eyes to the 4 main bosses(unsure of what this means though, coverage of the bosses is limited)
Twinmold can now be swung in a circle a la Bowser Super Mario 64 style but gets slammed in the ground
Fishing was added
Ocarina and pictobox have their own buttons
(if using new 3DS or Circle Pad Pro?) then full camera support
Some textures were changed
Garo Mask is now Garo Leader Mask
Masks can be organized?
Warp to any hour, not just every 12
Bomber's Notebook got changed. It's more in depth and you can set alarms now
Shiekah Stone Tutorials like in OoT3DS
The Bombers themselves now give you hints at different times of day to lead you to certain side quests and these add information to the bomber's notebook.
The sunblocks no longer have faces, now they have a single eye in the centre of the sun to denote you can use light arrows.
Magic arrows are separate items again instead of being subsets of the bow like in OoT3D
The Eye on Goht can be shot with the bow... whether this is needed to kill him or not has yet to be seen.
The Owl Statues now activate by walking near them, so you can save during the first three days.
There are Quill Statues for saving as well.
New masks?