If you go by VGChartz, and include remakes, it looks like this:

1. Ocarina of Time - 11.38 million
2. Twilight Princess - 8.75 million
3. Wind Waker - 6.03 million
4. Majora's Mask - 5.23 million
5. Skyward Sword - 3.96 million

Although without remakes, the order would be Twilight Princess, Ocarina of Time, Wind Waker, Skyward Sword, Majora's Mask.

Including remakes it a bit unfair, because 2/5 of the games have not had a remake (Except Twilight Princess HD is coming soon)

Majora's Mask sold 3.36 million copies while Skyward Sword sold 3.96 million.

Nintendo 64 sold 32.93 million units while Wii has sold over 101 million.


Although Skyward Sword technically sold more you have to put things into perspective.

I see the point your making. It's strange zelda sequels on same console seem to sell alot less than the 1st one out.  Also seems to prove people prefer TP, OoT adult link vs WW,SS, MM child and/or Cel shaded. And yet new Zelda still Cel shaded lol. Looks amazing though I do worry it will release too late and will have lost alot of interest and hype

But install base is only a part of a much, much bigger picture with regards to the Wii's twilight years.  Wii U announced, terrible droughts, a shot reputation with most gamers, no real promotion since around 2009, very, very little promotion for the game (which STILL boggles my mind), and on and on.  The Wii was in terrible shape in terms of perception and promotion by late 2011.  So yeah, gotta put things in perspective :P.

Well, by the second game on any console Nintendo tends to add strange things to Zelda that give the game less mass market appeal. Majora's Mask had the three day cycle, Skyward Sword had its art style and world structure and Spirit Tracks had the trains. 

Ocarina of Time and Twilight Princess were specifically designed to be grand, epic games that lots of people would want to play. Majora's Mask, Skyward Sword and Spirit Tracks were designed according to their developer's wishes. I think this is one of Nintendo's weaknesses: other developers are able to improve upon a game in the sequel, grow the game to become bigger and have a more widespread appeal. Nintendo does the opposite: When a game sells they use that as an excuse to make the sequel more niche. At least with Zelda. 

Majora's Mask is the worst selling. Skyward sword is most underperforming :)

Lucky it had Wii huge userbase to fall back on.

Yeah that's true. It's strange how they spend years building a new engine, and then rebuilt another engine for the next zelda game, alienating alot of fans who prefered the older style. Still I guess it helps keep things fresh, look at assassins creed for drop off in sales.

Personally, I think that's what makes the Zelda series so incredible and one of the best, if not THE best franchise in all of gaming.
The fact that it's able to take on and do all these different things, perspectives, and tastes, while the overarching formula that was established since the very first game of the franchise, still remains largely the same. And each and every game has been of high to extremely high quality, with every mainline console game being GotY candidates each time they come out, and Zelda Wii U will be no different.

Edit: And I don't say this just because Skyward Sword happens to be my absolute favorite video game of all time, (which I'm very proud to say it is.) I say this, because there is truth to it.
Next year will mark the 30th anniversary of the series, and it's going just as strong now, as it ever has been.
With that said, if Zelda Wii U remains Wii U exclusive, I think that may be the worst selling 3D Zelda game.
If it's also released on NX, then that could give it a chance to become the best selling 3D Zelda game (without remakes).

Twilight Princess actually was the best selling 3d Zelda game if you count both platforms it was launched on.

Skyward Sword was a great game and deserved better sales. But that's what happens when you release a zelda game on a downward trending platform.  You gotta release a zelda game earlier in a system's lifecycle IMO.

I wonder if SS will ever get a remake.  It would be difficult to do because the game requires a motion plus and nunchuck.