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.