Probably a combination of 4, 2, and 1, in that order.
Hypothetically: After OOT3D, Aonuma decided to have Grezzo also remake MM. But he wanted to release a brand-new Zelda for 3DS before releasing another remake (he said so himself), so he had them put it off for a while, with some devs doing preliminary work, preparations for the game. Maybe design ideas on what to add to or change in the game. After Four Swords and Flower Town were finished (June/July 2013), Grezzo started full development on MM3D.
Under 2 years doesn't sound like too long development time for this provided they make more significant changes than Ocarina 3D or Wind Waker HD had.