Aonuma said that development of MM3D started shortly after OoT 3D was released, in 2011

So my question is, why did it take so long?

Keep in mind Wind Waker HD was made in 6 months

Besides graphics, there really isn't anything that would make the development last that long

They changed some things up (Saving and bombers notebook) and added fishing, so why did that take 4 years?

What says you?

Just Nintendo being Nintendo

A small development team? I mean, it's not just a straight port you know.

Well, one thing to think about is that Majora's Mask 3D, compared to Wind Waker HD and Ocarina of Time 3D, is an actual full-fledged remake. WW HD and OoT 3D will likely be labeled as remasters, since they don't generally change very much except for the visuals. Majora's Mask 3D has many small changes to the game, including some of the mechanics. So it would make sense that it took longer.

Cause they wanted to release A Link Between Worlds first? Grezzo also made the lame Flower Town StreetPass game in the meantime. I'm sure they didn't rush Majora since A Link Between Worlds was the priority.

Probably because a small team was handling MM3D.

They were probably busy with doing other things as well

Windwaker HD was on a console with a similar architecture to the GC. N64 and 3DS do not have similar architectures. Lot's of code would have to be recompiled. Most of Windwaker's models and textures stayed the same. Majora Mask's textures and models changed quite a bit in the remake. That is without mentioning the gameplay decisions and changes.

Let people really want it by not providing them with it.

Once enough people want it release.

Also probably small team that took some time to make it and who knows how long its been done. They might just have waited to release it I mean bringing it out at the same time ALBW came out? or when WWHD came out? Not the best idea.

And maybe its their  2015 Zelda game so they have an "excuse" to delay WiiU Zelda into 2016?

It's probably because other Zelda games like Wind Waker HD and Link Between Worlds had more priority, and that Grezzo was just busy with other stuff.