Phantom Hourglass was my first but Spirit Tracks is my favorite. I actually really like the stylus DS controls (and it's not even that bad using a mouse on an emulator either) but the main thing I like is the music and story. Music and story I would say are both better in Spirit Tracks than any other game in the series. It also is one of the few games in the series that you can really call a legend of Zelda. She's there the whole time and the main story focuses on her character arc.
Just overall an amazing experience with some really dramatic moments, if I had to summarize what I like about it more than the other games in the series I'd say it's the most "cinematic & dramatic"