After thinking about it, I decided on Skyward Sword. Here's how.
Out of them all, Twilight Princess on Wii has probably the worst gameplay, due to the motion controls and the poor dungeon layout (not to mention the murky colour scheme* which makes darker dungeons into a long pixel hunt). However it is saved by the storyline and character designs**, which are probably the best in the series.
The most tedious in the series is probably Wind Waker, due to the almost endless sailing*** to get anywhere in the overworld. However when on land the game is absolutely brilliant and lots of fun, with gameplay which just works and a graphics style that despite odd looks great.
Overall I chose Skyward Sword because it inherited the technical problems of Twilight Princess, and didn't have a good enough storyline or anything else to redeem itself.
(* Its even worse when using Component video on an LCD TV, as the colour scheme was intended for CRT screens.)
(** I mean, who doesn't like Midna?)
(*** Yes, the Wii-U version does have a way to speed up the sailing, but its much less well known)