It shouldn't really be a question which game has better graphics. Technologically, the Wii is more powerful than the GameCube and naturally produces higher-quality graphics. Twilight Princess does not use graphics on the level of the Wii because it was originally made for the GameCube. When I played Metroid Prime Trilogy, I remember going from the second game (originally on GameCube) to the third game (originally on Wii) and noticing "wow, these graphics are SO much nicer." Even though they go through and increase the quality of the textures in the New Play Control games (of which MPT was one), the graphics originating on the Wii still look so much better. I'm not really one to judge the quality of the game based on graphics to any degree, but it was still something that I noticed.
In regards to Zelda, however, I realize that the difference isn't solely defined by the ability of the console producing the graphics. Skyward Sword uses cel-shading techniques like The Wind Waker, but on objects created in a realistic style like Twilight Princess. I personally think this is very cool. Rather than going the obvious way and choosing to alternate between styles, they chose to blend them in a way, and it looks very nice. I don't personally prefer one style over the other. It helps each Zelda game to really be its own thing. Having different styles from game to game makes them more unique than if they were to just use one style throughout the series. It's something that has really begun to help define Zelda. While most game series I play can be labeled as having either a cartoony style or a realistic style, Zelda is both at different times.
They've done something unique again with Skyward Sword, combining the two styles into one. In a way, it sort of creates its own third style. I think it's also very appropriate timeline-wise, where usually the Adult Timeline uses a cartoony style and the Child Timeline uses a realistic style. It's appropriate that a game that's before the timeline split uses a combination of the two different styles that exist after the timeline split. The whole distinction doesn't really work with the 2d games, but it does with the 3d games, where the whole style thing is more noticeable.
Returning to the whole issue of the quality of the graphics, I don't usually actually see a big difference in quality of graphics between GameCube and Wii games. I only really notice it when they're put virtually side-by-side like with Metroid Prime Trilogy. So, in terms of graphics quality, I can't say I really see any difference at all between Twilight Princess and Skyward Sword, though I still know as a fact that the Wii has better graphics than the GameCube. I like both styles as well. I'm not going to say either style is superior to the other because that would defeat the purpose of them both existing. I like them equally (though I guess it's really typical of me not to pick favorites).