Haha! Good choice at Wind Waker as #1. I agree by far most people get fooled by the cartoon graphics! Indeed some seriously disturbing stuff goes on behind the scenes in the story of WW.
Can't disagree with any of your reasoning, but personally I'd take the weight of each a little differently. My ranking of these ten would be (from light to dark):
Skyward Sword - Spirit Tracks - Legend of Zelda NES - Adventure of Link - A Link to the Past - Ocarina of Time - Twilight Princess - Wind Waker - Majora's Mask - Link's Awakening







