I haven't beaten Spirit Tracks yet, but I definitely like the storyline of the game so far. I'm about to enter the Sand Temple, so I've seen most of it by now, I think.
Some parts of it are very frustrating, but overall, the difficulty curve is more reasonable in ST than it was in PH. I actually enjoyed the Tower of Spirits at times, because it required you to use all your items and Zelda's phantom abilities in order to solve puzzles. Also, it had no timer, didn't require you to repeat floors after you'd gotten the map, and saved whether you used a key or not.
I also like hauling passengers and cargo in trains, except when I have to cross the Ocean Realm and face those pirate ships... they're a little overpowered in ST due to the limited maneuvering capabilities of the train relative to the ship in PH.