Phantom Hourglass with trains, less comedy and story, more fetch quests.
The story is incredibly straightforward with all the twists basically happening in the first cutscene. Zelda's body is taken to be used as a vessel for the Demon King, Malladus, by the creepy chancellor and you have to go to various temples to reestablish the titular spirit tracks across the land to weaken their attempts. Zelda's spirit follows you to act as your dialogue companion and by the end of your adventure you were just a hair too slow and fight Malladus. Nothing we haven't seen before, right?
Spirit Tracks uses the theme of a central dungeon that has to be traversed multiple times, a la the Ocean King's Temple in Phantom Hourglass, but it kept from growing stale and from artificially lengthening the game by removing the timed aspect and having set so that you can skip the parts you've already done by walking up the stairs to the next area.
The train itself controls fairly well, but it feels a bit slow compared to everything you can do outside of the train, not to mention the camera moves pretty sluggishly around it as well. The off-train sections control just as well as they do in Phantom Hourglass, in some ways better. All the response issues, like frantically drawing a circle for a spin attack without it registering, are still there, however. One good change to the stylus controls was the change to the rolls that Link does. Instead of having to draw a circle at the edge of the screen, a simple double tap in the desired direction is all that is required, which as I hinted at above has a higher chance of being useful.
The fetch quests are uninspired as well. Go collect stamps from towns and dungeons, catch rabbits in the field, do villager requests of ferrying them or their goods from point A to point B.
In terms of comedy and characterization, the removal of Linebeck, or a similar character is a detriment as the game tries to take on a slightly more serious tone. The case, though, is that it still tries to be funny in random increments, like the final boss fight or other tense situations. Zelda's shallow attempts don't quite nearly match Linebeck's ridiculousness.
Spirit Tracks is a solid title compared to most things out there, it just is about the least I'd expect they could get away with from something under the franchise name.