Well I haven't played 2, Oracle of Seasons, Skyward Sword, and the Four Sword games. So I can't comment on them. Out of the rest it was a real toss up between Twilight Princess and Spirit Tracks but Twilight Princesses is the worst.
The problems with Spirit Tracks is pretty much the almost game break badness of the train traversal but it did have some fantastic dungeons and really expanded on the game play of Phantom Hourglass which I really liked. Also having Zelda at your side of the entire game was a great idea. Overall I liked Spirit Tracks.
Twilight Princess on the other hand doesn't have anything as glaringly bad as Spirit Track's trains. But that game is far longer then it needs to be. The dungeons were ok but none really stand out to me. The Wolf Link mechanic wasn't good enough to justify all the backtracking it made you do. The combat felt like a step back from Wind Waker. Also it looks like a hot mess, its so muddy and jaggy. It aged very poorly and extremely fast. I would choose original OoT over TP for graphics anytime. On the plus side Midna was pretty great. Overall I feel meh about Twlight Princess so that's why it losses.