I've started Playing WW through again to see what went wrong in TP, and I'm seeing little things now that stand out.  For example, keys are displayed right in the corner of the screen in WW, why would TP hide them in teh pause menu?  Then I noticed HUGE things.  Things that almost made it seem like two totally different teams made these games:

Link is more smoothly animated in Wind Waker, every action seems natural as though an artist is drawing the game in real time.  The sword fights are more visceral, and enemies are more imposing not because they're threatening in looks, but the way they're animated give them a harder edge.  Armorghoma and Kalle Demos, are Wowzers of boss fights, the particle effects used when they move is sometimes distractingly stunning, and I'm surprised TP fails to capitalize on this.  The Stallord fight could have had dust particles floating past as Link circled the tower towards him, giving a greater sense of speed, I believe I remember Goht doing this.  But then Stallord has the worst dying animation ever in a game, he looks like he's trying to pretend like he's kicked the bucket, as he herky jerks his way down and then bounces unrealistically (read: awkward for a lifeless skull) across the ground. 

In fact, boss battles in general are more entertaining in Wind Waker, as though little touches like those, gave fights a faster feel to them, and Even though Wind Waker and TP both use Midi tracks, WW has more appropriate pieces, compare WW's goofy Jalhalla (the Ghost boss) who has what sounds like an opium driven background piece, to Twilight Princess's Stallord who's music sometimes even seems to dwindle away to nothing.

Link in WW has more personality, and his cutscenes are more evocative and moving, with WW's story of course you're going to be moved, but the cutscenes explaining the extinction of the Kokiri and Zora people are really touching.  Similarly to how Majora's Mask was primarily a game about Healing, WW seems to be a game about sacrifice, people had to make do and survive as best they could.  I can't seem to nail down what TP is about really, but the closest I can get is a purging of sorts, cleansing.  Which doesn't make for good emotional fare.

But, TP just feels like a 10 year old game in GC graphics.  OoT had better Horse animations, now Link looks like he's impotent thanks to Epona as he bounces around.  Go back and Watch the E3 videos where riding Epona looks more natural for TP.  Link runs with his arms stiff at his sides, not good for building momentum.

Everything about TP feels...Off.  Like, they had the game right but then made little mistakes, or didn't make an extra effort to make the game better.