Yeah, the Spirit Tracks hate is just baffling. It has good dungeons and puzzles, one of the best soundtracks in the series, a wonderful refreshing story with the best Princess Zelda in the series.
I get that the train is a bit slow, but at least it was engaging. In Wind Waker and Phantom Hourglass you can just aim at the next island and take a nap most of the time and it takes just as long, but with the Train you have to watch out for those enemy trains that give you an instant game over if they get you. It's tense.
Hell, I only rented Spirit Tracks and in the few days I had the game I beat it, got all the gold train parts, and did a good chunk of the other sidequests. It blew me away how heartwarming it was and I couldn't put it down.