Finished off the game last night, and have some quick takes based on my experience (with spoilers hidden for those still playing):
* Riding the rails is a nice novelty, but becomes increasingly time-consuming and annoying as the game progresses. Sure, you unlock new paths and warp points, but they rarely save significant time and all too often have the opposite effect - giving you remote areas you needs to drive through at least once.
* Optional content and side-quests aren't nearly rewarding enough. Some of this is tied into finding the overworld tedious, but it's also because upgrades in this game just aren't empowering or interesting. The player is often asked to do a lot of work for little reward, and without much in the way of story justification. I tried to get invested in solving problems for people... but eventually gave up. There just wasn't a good enough reason to spend literally hours on lame fetch quests
* Sub-weapon selection is pretty good in this game! I like the whip, although find it might be a bit underused. and blowing in the microphone to create little tornadoes is kind of fun. The sand wand is also pretty cool and creates some nice sense of verticality in the game, although is another case of a power that could have been used more in my opinion.
* The last boss is absolute garbage. It combines everything that isn't fun about the game into one long and awkward battle: escort mission, precision touchscreen controls in combat, DS microphone, and then more teamwork battle... I really like it when the DS Zelda games have big, bold bosses that span across both screens. The last boss in Phantom Hourglass was impressive, and some of the earlier bosses in Spirit Tracks were pretty decent too. But this final boss was garbage - hot, steaming garbage that almost convinced me to just put the game away and call it quits because the whole encounter just wasn't fun. One upside: the train challenges going in to the final boss were kind of rewarding.
Overall, I can only think of one portable Zelda game that I enjoyed less than this game: Oracle of Ages. The game started off slowly and didn't really impress early on. Some of the novelty won me over during the mid-game... but then wore thin far too quickly, and by the end of the game my opinion had once again soured. Despite the game doing some interesting things, having a bad start and end is just too much to overcome...
So yeah, not sure what to think about Spirit Tracks overall. I guess that it's good to have finally played through so that now I can try to sell the game? Hopefully prospective buyers don't read this comment first though, because I wouldn't recommend that any of my friends spend the time/effort to track this game down.