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I can't decide between those two. Skyward is just so much fun and when it comes to "Who is the better Main Villain?", Skyward definitely wins with Ghirahim. Because Zant was just a joke towards the end. But I also loved the art for Twilight and the dungeons and bosses. I never played the Wii version and I don't want to... so I can't say if TP's motion control was better, although I heard it wasn't.
2: Wind Waker
Sailing was boring, the Triforce of Courage collecting was boring, but it was still a very fun game. I don't think I ever did a 100% run on this, although I am currently stopping plot advancement to get a ton of Figurines done.
3: Ocarina of Time
I'm only putting this here cause I don't like Majora's Mask that much. Otherwise, it wouldn't be on the list. The controls are clunky, the dungeons... urgh, Forest dungeon has really annoyed me and I haven't even gotten to the Water dungeon yet. I am about to... I am so tempted to skip over the last dungeons and just cheat the medaillons into my inventory.
Cloud and Sephiroth - battling each other since '97 for your amusement Give it a rest already!