Well, I recently played Phantom Hourglass, so this was obviously next on the list.
First of all, a lot of the problems I had with the first game were fixed up a bit. The controls have been tidied up (rolling especially is easier) and the GUI looks much nicer (maps are more colourful and accurate). The plot and music are also much more memorable than before. Phantom Hourglass felt like a crappy handheld version of Wind Waker in many ways, but in Spirit Tracks I didn't feel that way, probably since it's a new generation of characters and a new style of travel.
I also really like how Zelda is finally a useful character. Couldn't stop thinking of the team as Ed and Al from Full Metal Alchemist. Zelda's a true bro, right down to the final battle. Toon Zelda better be playable in the next Smash Brothers.
Also, that magic wand you get was a fun item.
Anyhow, despite the improvements, plenty of new problems were introduced. Spirit Tracks uses the microphone a lot more than Phantom Hourglass, which is bearable for the wind item, but really frustrating when using the pan flute. The 3DS has the microphone down in the corner, so blowing into it while fiddling with the stylus as well is damn frustrating. I had to switch over to the DSlite for the final song, and even then it was still hard to play. I consider the pan flute the worst Zelda item ever made.
The whole train thing was fun for a while, but when you had to start revisiting old areas, getting destroyed by other trains, or hunting down rabbits, it all got a bit annoying. I don't think I'll be doing any of the side quests.
The final dungeon was also long and tedious as hell, involving lots of backtracking and boring puzzles. Although phantom Zelda usually controlled quite well, the "call" command often failed to work properly, with Zelda jumping into sand or being unable to figure out how to use stairs.
Overall I enjoyed most of the game, but a few parts really got frustrating.
Next up: Minish Cap.
Also, I think I'm in love:[link] [link] [link]