Spirit Tracks is a great game with lots of content to keep you going for a while, but not everyone will enjoy this game.
The story starts off really well. It sucks you in, gets you going. But, the story pauses and you don't find anything out until about 7 dungeons after, and even then, its just short little bit and it gets cut off. So.. more dungeons, then it goes smoothly. But I didn't mind that as much because you were occupied during those gaps, and I wouldn't say that's really a reason to not enjoy the game.
Dungeons are great, but half the dungeons are really easy. But it does give you a jump in difficulty that isn't enough to kill you but puts it up to a point where you finally get to see some of that classic "running around the room trying to figure out what the crap to do to move on" action that Zelda games are great at doing to you. But I felt even the final dungeon could have been just a bit harder.
Train. This is the part I know at least I was a bit worried about. It is more fun then I expected. It was well executed. There are lots of places to explore, lots of little secrets to find while traveling around Hyrule. So unless you are 100% against the idea of travel by train in a Zelda game, there really isn't any reason to worry about this part.
The control system is actually great. It's responsive and fun. It was very well executed. And it didn't get annoying. And controlling Zelda with the stylus was fine too, in fact, it was excellent. It added an interesting new aspect to the chain of dungeon the Phantoms are involved it and it keep you on your edge, you have to think about both characters. They focused a lot of boss battles around using both too, and it works. It's never frustrating, it just requires some reflexes. There are pathfinding issues with Zelda, which did tick me off.
So I would recommend buying this game. Its certainly worth it. No annoying timed segments like in Phantom Hourglass. So I would only avoid this game if you are against the train.