From the first few hours of Spirit Tracks, I preferred instantly it over Phantom Hourglass. It has some nice throwbacks to Phantom Hourglass, the villains are actually more interesting than Bellum, and while I'm sure Zelda's personality would be a bit of a negative point to some, it's better than the small role Tetra played in PH. The Tower of Spirits isn't timed, which addresses one of the main problems of the Temple of the Ocean King. The game has less dungeons than PH, but the level designs make up for that. When you try to move the Big Key, Floormasters appear and try to take back the key, so you have to fight them off. It's essentially the last challenge just before the boss fight. I really can't think of anything that PH did better than ST other than how PH improved the sailing in WW, whereas ST requires you to draw particular paths along the tracks, but if you want Spirit Tracks to be better than Phantom Hourglass, I'm sure you won't be disappointed.