I liked Phantom's Hourglass, but now it feels like it was a prototype and Spirit Tracks is the real deal.
It is surprising that a game can be as good as this when it is controled only with touch screen and stylus. There are very few issues with the DS misreading your taping. Only when firing bombs as your train is turning or when firing at a certain enemy you meet in caves will there be problems. If you take some of the harder side-quests though, there might be some more.
I think the most important improvement with Spirit Tracks is that it's very inspired. The story is very good, the artwork is amazing and they half the items are new - a lot for a Zelda game. The music might be the best improvement though. There is a lot of brilliant tracks and only the Goron soundtrack is a remix of old Zelda tracs. Once again - a lot of innovation considering it is a Zelda game. The Spirit Pipes make this the first hanheld zelda game with a proper instrument, and to me it even tops the ocarina from OoT and MM. I wish there were more songs to learn for the pipes, but when you play the pipes with the Spirit Guardians called Lokomos it is heaven for the ear.
All the major flaws from PH has been fixed, leaving a nearly flawless result. The main dungeon - the Tower of Spirits, is less repetitive since it has a central staircase so there is no backtracking. The train riding is much better than the sailing and if you stick to the main quest I doubt you'll get tired of it - but if you want to take the side-quests, which there are tons of - you probably will be. Even when it comes to things that weren't a big problem, they are improved. The dungeons are better, and I like how puzzle-based they are. The boss fights are a lot better. The treasure system has more treasures and they matter more because you trade them for train parts.
Some of the side-quests are awesome. If you fought the main quest wasn't challenging enough, try the Gerudo's challenge in Hyrule town. Also, the mini-games are some of the best in the series.
What more can I say, Spirt Tracks is amazing and tops all my exceptations. A well-deserved 9.5.