The answer's gotta be Twilight Princess.
For all of its faults, Skyward Sword had some of the best things in the series going for it, the greatest of which is in the portrayal of Zelda. I was at first skeptical of her "schoolgirl" look, but from minute one, as in no other Zelda game before, I didn't only care about saving her again this time, but as the adventure moved on I began to fear for her. Then that touching scene rolls around... I'm a grown man and let me tell you, I can still cry
Skyward Sword gets considerable credit for Zelda's portrayal, but SS was unfortunately lacking in many of the things that appeal to me most in a Zelda game. Regardless of the shoddy controls, which were the biggest issue, and while the redesign of traditional Zelda series structure had its merits, Skyward's graphics, while beautiful, did not lend itself well to conveying the fantastic feeling of a magnificent fantasy world, nor did Hyrule even remotely resemble the land as we've ever seen it in appearance, regardless of presentation. Great and innovative gameplay, a big redesign for better
and worse, and a fantastic portrayal of Zelda and still it's not the greatest.
Which leaves Twilight Princess to shine as the Wii's best Zelda title. The best since Majora's Mask, imo. It harkens back to everything that appeals to me in Ocarina of Time and Majora's Mask. Midna makes for a fantastic character who still puts Skyward Sword's Zelda to shame. It suffers more than some of the "best" Zelda games, though still far less than Skyward, but manages to have that which appeals to me most in a great Zelda adventure!