Cel-shaded graphics, sailing, and some new sword techniques makes Wind Waker a force to be reckoned with.
As for sailing, it's a double edged sword. Sailing can easily get tedious. You will get warps, but that won't help much. What sailing across the big blue does do is create a huge world to explore. Lots of islands and plenty of sidequests make this game great for perfectionists.
As for the main story, IMO its much more engaging than Twilight Princess. The final battle is truly an epic one for those who completed Ocarina of Time. The normal quest only has about 7 dungeons in it, but with sailing and things to do before each dungeon, it's truly a lengthy game.
This time around it seems Nintendo paid more attention to each character's personality. The final boss is a great example. His facial expressions really make the boss a force to be reckoned with. On the flip side, when he talks about his past you can really sympethise with the boss. 2 sided story. While we think of the wind as something that brings peace, the boss opens up a new side of the story, the wind bringing suffering to his people. Basically, the story telling makes WW epic. Final boss, truly epic.
If you skipped WW due to graphics and whatnot, you made a mistake.
SPOILERS for WW and TP
I believe Ganon was given the triforce of power when he was to be killed by the sages in TP, to get revenge on his people. My theory anyway, since TP seems to come before WW.