Maybe Nintendo misplaced the original code.

What others have said, likely they were busy with other games and MM looks like it had more work done on it. It looks more like a remake over a remastering.

I've wondered this as well. When I heard development began right after OoT 3D came out, I thought there'd be major changes, like new dungeons and side quests, but that's not the case. Based on the changes they did make to the original, I'm really not sure why it took almost 4 years to make.

Because they were waiting on the moon.

I know they mentioned that they wanted to do a new Zelda game in between the two remakes, hence Link Between Worlds in 2013. But why it took them until this month to release it, not sure. Would make more sense to have released it in November last year. Maybe split development for Zelda U, so it took longer than OoT 3D and WW HD.

No, it's right on time. Zeldas need to be spaced adequately.

They probably didn't have enough time to work on MM3D since they were busy on other games like A Link Between Worlds! Nothing out of the ordinary me thinks.