Well Wind Waker's aesthetic is, to me, on a playing field all its own. It OWNED the Zelda aesthetic, its animation (particularly facial) is unmatched to this day in the franchise and it actually married the serious and light hearted in a near perfect harmony at the end. It was quite elegant, really. I think in regards to 'covering up its flaws', I think Wind Waker would have been near the perfect Zelda if they simply made it more difficult and added back in those two or so dungeons that they didn't have time to patch in. That's to me all that was missing (oh, and make it so you don't have to constantly change wind direction to change ship travel direction). Wind Waker, even back when it came out, instantly disarmed me with its brilliant artistic direction and stellar list of improvements to the Ocarina of Time gameplay formula, which to this day represents the best "mixture" of old and new. I still vastly prefer its combat to what we have in Skyward Sword and TP introduced some new problems, so WW is the right chord.
Skyward Sword has the best bosses in the franchise, however, and some of the music is top tier. And its art direction is a good compromise between the two classes of Zelda styles, but I prefer Wind Waker's.
The more subtle animation in character movements is definitely better in Skyward Sword, but I still think facial animation wise Wind Waker is king.
I'm constantly wavering between choosing WW and SS as my favourite in terms of aesthetic. WW definitely wins in regards to facial animation because of the extra amount of stylisation involved but I adore SS's paint filter and the constant texture detail.
In more general animation terms I find it even harder to decide; I've always felt like WW's characters are the most charming of any Zelda but all those extra touches SS has makes it hard to decide (I love how the item shop guy reacts to what you do). It's too bad that these little touches are wasted on otherwise empty characters.
I'm honestly not sure if I'd want more Wind Waker aesthetic in my Skyward Sword or more Skyward Sword aesthetic in my Wind Waker.
My list of actual gameplay issues with WW is a bit longer though; I prefer SS's larger, more open dungeons (as well as their internal variation) to WW's small-room-to-small-room thing.
And I love SS's blurring between overworld and dungeon. I do wish they'd gone even further with it (since I was imagining something like Ico when I first heard about it) but it's a huge improvement over WW in that regard.
I prefer the sailing in WW though. Even though flying in SS is a lot more involving I find the sky to be far less interesting to navigate. It could do with either being smaller or having more towns. Actually I'm surprised that SS manages to have less towns/islands than WW. It almost balances out since SS's sky is a lot smaller but yet, oddly, it still feels far more barren to me. Huge improvement over TP's overworld though.
Combat wise, yeah WW's my fave too. TP generally felt like a step backwards and while SS is a nice change it largely feels superfluous. It's like they've given depth to a combat system that needed breadth. Why not actual combos? Optional sword techniques you can find and upgrade? Hell they've got elemental enemies in SS, why not elemental sword techniques to counter them? Why not integrate Links new agility more into the combat?
I still think MM is the best in terms of story/characters/world building and side quests though. WW can't touch those aspects of MM and sadly SS is worse (especially since they removed day/night cycles and weather).
But yeah WW's being given a good run by SS as far as I'm concerned. I'm doubting it'll be able to top WW's ending though.
