A 3rd Hero of Time game set in an entirely new world with entirely new races but still utilizing the mask transformation system from MM would be amazing. I actually could see it coming to 3ds, but being New 3ds exclusive. With the success of N3DS so far and all the 3ds games on the slate this year, I don't see support ending for it anytime soon. Maybe for the 3DS, but I definitely think the N3DS will continue getting big games for another 2+ years.
Here's a wild idea: what if Nintendo knew all along they wanted to make a third Hero of Time game for 3ds, but felt the need to re-release OoT and MM on the system first since they're older and several modern gamers may not have played them. Hell, maybe this 3rd HoT game has been in development nearly as long as MM3D, and that's why it took them so long on that one. They were kind of splitting dev time between the two. Of course I'm sure I'm just dreaming, but interesting to chew on.