That's what I've been wondering.
Ocarina of Time is already a bigger game, and with OoT3D also including the Boss-mode and the Master Quest, having just the original game in MM3D would make it a little lacking in content...
I'd say a classic SS/WWHD-style 'Hero Mode' is a given at least, but I really hope they'll redo the dungeons as well to have something comparable to Master Quest as the standard Hero Mode adds little value.