Wind Waker. In ever single aspect.
Graphics: I never really cared for how realistic graphics are. What's more important to me is how well they convey the action of the game, and WW's simpler graphics did a far better job of it than TP's graphics in my opinion. Because of the simple cel-shading, WW was able to focus a lot more on the details in the animations, like how Link's eyes could point towards important environmental elements or how characters were so much more expressive. TP's graphics felt unpolished in comparison, and at times were just a bit too dull for my tastes.
Gameplay: WW's fighting mechanics felt overall so much smoother than TP (I played the Wii version, can't speak for the GC). The WW parries flowed beautifully and the items made for much more comfortable attack combos. The WW Boomerang and Grapple Hook remain two of my favorite items ever because of the way they were used in battle. TP's motion controls were kind of clunky, mostly a lot of flailing around, not really any precision. While I loved being able to point and shoot with the wiimote, there were just too many other unnecessary weapons. Also, in the enemy AI department, WW was far superior. WW's enemies could interact with each other and the environment in ways enemies in no other Zelda game so far could. WW also had epic teamwork mechanisms in the Sage Temples, and WW dungeons just felt more fun to me overall than TP's dungeons did.
Overworld: TP's overworld was huge and beautiful, and WW sailing was dull. I will admit that much. However, I in no way agree with the sentiment that TP's overworld had enough in it to do. I felt that TP's overworld was wasted space; all it really had were a few sparse caverns with nothing but enemies or really simple puzzles. WW on the other hand had half its islands as optional areas for free exploration. Though there was a lot of empty space in the Great Sea, the volume of islands to be explored made WW's overworld feel more substantial than TP's Hyrule Fields.
Difficulty: A moot point. Both were around the same difficulty level to me. However, WW felt less tedious. All it had that was repetitive was Triforce Shards, and only the deciphering/salvaging portion. That took no time at all compared to TP's Tears of Light.
Story/Characterizations: WW was a lot more balanced in this regard, and I felt the main characters had a lot more characterization than did TP's main characters. TP had an excellent character in Midna, and an excellent one in Zant for the most part (I hated him in the second half though), but both Zelda and Ganondorf had very little in the way of personality. They were both sort of there, cliche'd princess with a serious demeanor and cliche'd villain with a greed for power. WW's Tetra was snarky and all around awesome, King Daphnes had such a deep philosophical character to him, and Ganondorf was actually given a real motive beyond just the whole power-hungry thing. As a side note, VM me if you see this sentence having read this whole thing. I want to give you a cookie for reading it all. Anyways, the story themes in WW were so much deeper than those in TP, and WW spaced out its storytelling much better than TP did. TP lost a lot of its storyline during the second half of the game. TP did do better in the side character department though, especially with Colin, but he got so little screen time that it doesn't count for much. Characters like Medli proved so much more likeable.
Side content: Collecting enemy spoils in WW just seemed so much more entertaining than running around looking for poes in the dead of night or tiny golden insects hidden goddess knows where. I've also already talked about how WW had so many optional islands with their own fun things to do; it was so much more open to letting you do whatever you felt like. Both games had their fair share of minigames, and there were many in TP I really really enjoyed (snowboarding for example), but I kept getting turned off by how the vast majority of Castle Town had nothing for you to do, just filler space. This is compared to Windfall Island, which is an absolute hub of activity and everything on the island is there for a reason.
Music: Wind God's Aria and Earth God's Lyric. 'Nuff said. But seriously, I guess I'm a sucker for upbeat string music. I honestly cannot remember much of TP's music at all, save for a few classics like Midna's Desperation and whatnot, but WW had more memorable music to it (Dragon Roost anyone?)
If you can't tell by how much I wrote, WW is very high on my favorites list and I have many many issues with TP. Thus, I am extremely biased on this matter. =/
tl;dr: I love WW with a passion.