After beating the game, I have to say, this COULD'VE been the 3rd best Zelda game I've ever played (replacing Minish Cap).
The puzzles were way better than any Zelda game ever. The boss battles were a million times better and more difficult than console Zeldas. The game was really long, and the story wasn't too bad. There were a couple of things that completely screwed up the game for me though. I don't know if we still need to put up spoilers, but whatever. There are spoilers.
The whole concept behind the train is completely flawed. I mean, why didn't the stupid Spirit Tracks have two lanes? Were the Gods really that dumb? Did the almighty Gods not foresee oncoming traffic becoming a dangerous and expensive issue? Did the Gods really expect me to stop Malladus using those tracks? Other than that, the train moved way too slow, and the Magic teleporter things weren't useful at all (I only used it once in the entire game). The train scenery wasn't interesting at all, and the enemies you had to fight were more of a hassle than a sneaky way to make the train ride seem shorter. All of my sessions with this game ended with me getting on the train. Seriously, instead of clicking on Zelda, I would just close my DS. The train was just a terrible experience and I hated it, so, so, soooo much.
Another minor thing that bugged me was the flute. They had no mic sensitivity settings anywhere. There were points in which playing songs was pretty much impossible because of the background noise (or in my case, the car air conditioner that wasn't even blowing into the mic >_>). Then there was the issue in which sometimes, the screen was just simply too small, and I couldn't reach some notes without letting go really fast. They should've made the flute slightly smaller.
I also had an issue with the songs not being used immediately when you learned them. I made a post about it a while ago, relating to the Regal Ring and the Song of Discovery, in which you're supposed to learn the Song of Discovery early on in the game, and use it much later to dig up the Regal Ring. Although the whole fiasco for not learning the song when I needed to was mainly my fault, I can still put fault in the game in the sense that there was no puzzle making sure that I didn't run off without it. It could've saved me the 40 minute train ride all across New Hyrule.
And last but not least, the multiplayer doesn't use WFC. A huge setback from Phantom Hourglass.
I give it a 5/10. The game minus the train is phenomenal, but with the train, it severely lacked. The game became a chore to complete, and I got sick of it after beating about 5/8ths of the game.