Also, TP came out when the Wii was first launched. The install base was relatively miniscule at that point. SS came out when the install base was at a peak, and still managed to sell less than Wind Waker. 

No the art style doesn't affect the sales, even though I believe the only time it really affect the sales was with Wind Waker. SS sold less because:
-you need motion plus
-bad controls for some fans
-And piracy

Wait so are u saying install base doesnt matter then going on to say it does in ur next sentance?

No. In the first sentence, I say that a game doesn't randomly sell way better because of the install base. Of course it sells better, but most Nintendo series on the Wii didn't sell double (Or more) of what they did on the GameCube. 

What I mean in the second sentence is that much more people bought a Wii, giving Skyward Sword a better chance to sell than Majora's Mask got.

No it didn't. It sold 1/3 of what WW sold on the GCN. SS didn't sell as well because the Wii was dead when SS came out, and the motion control fad was already over. If SS was the lauched with the Wii instead of TP, it would have sold just as well. If TP was launched in place of SS, it would have sold just as mediocre. TP is also criticized for being having an ugly color pallet and aging terrebly. The GCN version did not have "unprecidented sales."

And selling 3.75m units on a dead console using a control scheme people came to revile years prior is not a "flop."

As a Zelda expert, yes. You can even see after the great style for Zelda U that some still complain about not getting TP 2.0.

Many gamers like their mature (pfff hahahahahahahaha) artstyle, in other words, brown.

The Wii motion plus ad-on came in June 2009. November 2010 the wiimote plus was bundled with every new console. The plus controller was only used for six  five games essentially:
Wii Sports Resort, Wii Play Motion, Red Steel 2, Fling Smash, Wii Fit plus and Zelda SS.
I have not seen any reports on how many wiimote plus that were sold.
A simple addition of games sales gives us :
32 + 1 + 0.5 + 0.5 + 21 + 4 = 58 37 millions.
So the user base for buying Skyward Sword may be somewhere around half of the total Wii sales numbers.

EDIT: Wii Fit Plus did not use the Wiimote plus did it?

It was also a little late... Nintendo hadn't really released any major games for over a year.... Between SMG2 [mid 2010] and SS [end of 2011] the only games Nintendo fans could get excited about were DKCR and Kirby, both of which were late 2010 (ie still a whole year before SS) and the latter is almost niche compared to other major Nintendo franchises (kinda surprised it managed 2 million tbh)

As much as I hate to say it, the Wii hype had died down by that time.

Wind Waker and Skyward Sword sales tell the truth, especially since both are great games with very bad sales. I for myself cannot stand the Wind Waker art style so I never really played that game and sold it.

Zelda does not need to be dark to appeal, it just needs to be realistic.

The Wind Waker is my favorite Zelda game.

However there is no denying the fans want a graphical style closer to Ocarina of Time and Twilight Princess. In fact why Nintendo is going with the ugly Skyward Sword graphics after their E3 demo a couple years ago is a mystery to me. Heck I'd prefer Wind Waker style.