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Each of them has one big flaw. In Phantom Hourglass, it's the Ocean Temple. But in Spirit Tracks, it's the whole damn overworld that was replaced by a few rails. Riding the train was a pain, and the exploration aspect and the feeling of being in an actual, big, living world was completely killed by this decision. 

Apart from that: ST has the better dungeons. PH has the less ridiculous setting. 

My vote: PH is better, but both games are lacking in scope, overworld depth and sidequests.