Skyward Sword was badly conceived, period. Internationally speaking, Twilight Princess was one of the most successful Zelda releases of all time. Releasing it together with the Wii benefitted the game greatly everyhwere -- except in Japan, where it failed to sell as good as its predecessor, but still sold a solid amount of copies.
However, Phantom Hourglass's success in Japan apparently lead Nintendo to believe that a "cartoon Zelda" is more appealing to the Japanese market than a "realistic Zelda". At the same time they knew farely well that it's the other way around in the rest of the world. Skyward Sword was born. It reflects Nintendo trying to combine Wind Waker's/PH's comic look with the more realistic approach of Twilight Princess. A style that was supposed to appeal to both east and west, to children and grown-ups alike.
Suffice to say that this failed. Instead it's a style that's largely not regarded as appealing by most people on either side of the world. Skyward Sword is kinda similar to Majora's Mask in regards to its sales: It followed one of the most successful games in the series .. and somehow ends up to become one of the least successful entries. It's worse this time around though, since SS was in development for an eternity.
Zelda is probably the one series where Nintendo should, for a change, stop making weird experiments and just listen to the criticism of the fans instead. I loved Skyward Sword, both its gameplay and its looks, but it's easy to see that it's not the game most people actually wanted. In the worst case, it might be a good idea to disregard the Japanese side of things entirely for this series. Twilight Princess managed to sell 8m worldwide, eventhough it just sold 500k in Japan, after all.
I wonder if that's even true. Both Minish Cap and A Link to the Past GBA didn't exactly set the charts on fire, despite being in 2D. I don't think it's entirely unlikely that Phantom Hourglass mainly benefitted from the immense popularity of the DS at its time. Spirit Tracks still sold well, but that was rather overshipped and sold for a few bucks a few months after release.
Link Between Worlds shouldn't have a hard time out-selling Skyward Sword, though. It will definitely benefit from being on a plattform that's not already kinda dead at the time of its release.
While your analysis about TP/SS raises some good points (though I disagree about SS artstylme), you also forgot to mention one of the most important reason for SS great-but-still-rather-lukewarm sales : it was released very late in the Wii life-cycle, at a time where the console popularity was plummeting (especially among "core" gamers, the main target for Zelda games). That really had a huge impact, because by that time, third-party support had pretty much non-existent for months, and Nintendo output wasn't hot either (especially in Japan).
Besides, one other thing you forgot to take into account : WiiMotion Plus. Any game that required an add-on to be purchased separately will ALWAYS have some trouble selling. And no, not everybody bought one before thanks to Wii Sports, as it rose to n°1 on Amazon best-sellers on Christmas day (FR).
Problem with Zelda is similar to 3D Mario : differences in taste between Japan and the West.
And about the Zelda experiments and what Zelda fans want...
- Zelda fans wanted dark/mature Zelda with realistic graphics and lots of dungeons > TP
- Zelda fans wanted some RPG elements back in the game, more customisation, more stuff between dungeons > SS
- Zelda fans wanted a sequel to ALTTP, a top-down Zelda like the traditional 2D Zelda : > ALBW.
Yet, you'll find fans complaining about all games anyway. Listening to Zelda fans criticism is all good, but the Zelda fanbase tastes are so diverse, Aonuma and co can't possibly make something that'll please everyone... which is probably one of the biggest challenges the Zelda series is facing at the moment.
Focus on the West? Japan? 3D? 2D? Open-world? Lots of RPG elements? Less Puzzles? Whatever they do, they won't be able to please anyone.
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Ooops. my bad, didn't want to derail this thread. I got a little carried away
About The Wind Waker HD, it sure doesn't look good in Japan... then again, that's hardly surprising. Most Wii U projects don't look good in Japan at the moment.