I go with Option 2.
OoT 3D helped the 3DS to become such a success it is today. So maybe Nintendo thought to remake MM, too so that more people will buy a 3DS. The team started working on the new project but the 3DS became a success anyway. But then Nintendos Wii U wasn't the great success Nintendo expected. So they decided to concentrate on Zelda games for the Wii U. They worked on WW HD and more people started to work on the next Wii U Zelda. MM wasn't the most important project because Nintendo needed and needs games to help the Wii U. That's why it took such a long time for MM and it wasn't necessary to hurry up because the rumors and the growing hype about a MM Remake were the best advertisement and a sign that the remake will sell well anyway. Anytime.
I don't hate Microsoft, I don't hate PC,
I don't prefer Sony, I don't prefer Nintendo.
...Ok, I love Nintendo but this is something about tolerance, ok?
I'm a gamer with one of the greatest hobbies and I want to share this greatness with everyone.
