As I haven't tried playing PH yet, I cannot decide how ST compares to it, like some of the others here. ST was my first foray into handheld Zeldas, so going in I was only used to the grand console titles, like OoT, MM and TP - so just trying out ST the first time was a huge change for me. But I was surprised to see how much I ended up enjoying it. Sure, I can understand some people not loving the stylus-controls and I have to say I got a bit lightheaded whenever I had to play the flute as it took me a while to understand what strength and angle I needed to blow in order to make the damn instrument work, lol. But once I got both things under control, I really enjoyed it.
The train is a new and exciting method of traveling and sure, it can be a bit tedious at times when you have to travel far (but thankfully there are several nice warp points where you can go from one land to another without having to physically drive the train the whole way), but I loved the customizations you could do (I, of course, made sure to get the complete dragon train set). I also loved how you uncovered more and more train tracks as you did favors for various characters, making the journeys easier, as well as giving you the chance to explore previously hidden locations. The bunnies were fun, despite sometimes being frustrating to try and locate them all. And something I really loved was Zelda's own participation in the game. That was really refreshing. It made gameplay more interesting, made for some great puzzles. And the boss fights were awesome as ST utilized the two screens in a really great way (I really loved how ST was part 2D and part 3D in terms of gameplay)
So yeah, as someone who was prior to ST used to only the console titles in Zelda, I can completely recommend ST. It's really enjoyable