The Legend of Zelda: Wind Waker 
The Legend of Zelda: Twilight Princess Overall Comparison To begin with, both of these games are totally awesome, but I personally find that Wind Waker is the better of the two. The gameplay being so similar between two Zelda games, it ultimately comes down to the details, and I have to say I think the world of Wind Waker is much more interesting and engrossing. I found the sea exploration and treasure-hunting aspects of Windwaker lacking in Twilight Princess, which ultimately felt more linear. Finally, as a matter of personal taste, I even prefer the cel-shaded style of graphics.
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However, I will give Twilight Princess credit due to the boss fight against Ganon and the throwback to his more porkalicious days. Turn back from wolf to human was just tedious, and I hated how you couldn't just teleport as human (Hylian, whatever). The items were nice though, especially double clawshot. However I still prefer toon Link's grappling hook.
I don't like that they put a curse on Link to where he became a werewolf, as far as I'm aware nothing like that has ever even been HINTED at in the franchise (Despite the MASKS which were easy to change to and from in Majora's Mask). So sure, both games are fun..and both have flaws, but In my opinion Wind Waker wins this one