I really liked Spirit Tracks.

Train gameplay was actually enjoyable for me (especially the way it got used in one of the end game fights was so cool). It was also nice that Zelda was an actual part of the game and an actual partner that was part of the plot and helped solve puzzles instead of some princess locked away in a castle.

I played Phantom Hourglass much later and Spirit Tracks honestly just felt much more polished and fun.