Well, Chalts, I'm glad you said that since I'm working on my own fantasy story right now that has technological progression different from that of our own. And don't think I didn't see the potential hypocrisy in my earlier statements as I was writing them. However, The Legend of Zelda has classically represented itself as a world nearly analagous to a medieval fantasy world. It wasn't until Link's Awakening (a side-story) that any kind of anachronistic technology was introduced. Since then, there have been neon lights, complicated machinery, and now trains. While Zelda technically can get a pass on these things by sheer logic of it being fantasy and not tied to our world, it seems to be trying to be too many things at once lately.
The most interesting defense I've seen of Spirit Tracks is that technology would progress from the first game, so trains would eventually be feasible. I would like to take a moment to say that the Mario games seem to be subject to the same technological ramifications, where the Mushroom Kingdom seems to be quickly evolving from an old-fashioned fantasy kingdom to a much more modern one. While that occasionally seems a bit difficult for me to swallow, I can more easily go along with it for two reasons: lack of continuity and lack of attempt of realism. The Mario series is intentionally goofy and cartoony to a much greater extent than any entry in the Zelda series, and hardly any Mario game has any kind of narrative connection to any other Mario game. Therefore, Mario is much more of an open slate, and they can pretty much do anything with him.
As for Zelda, while they don't maintain a heavily-connected timeline, they have created a timeline and, in recent years, connections between entries in the series. While it's never been presented overtly or as a huge deal, it is something that significantly separates the Zelda series from the Mario series. Continuity does exist. To that end, the argument I mentioned above falls apart since most Zelda games of recent years have been prequels or put towards the beginning the established timeline. In fact, the oldest games in the series seem to be the most chronologically recent. And we've seen the world they established: extremely medieval-like with no anachronistic technology save for magic.
Granted, my entire argument could easily fall apart either by my lack of knowledge of the actual game or by future retcons in Nintendo's arsenal. I don't know where on the timeline Spirit Tracks is supposed to be (although I assume it connects to Wind Waker Link), and, even after all these years, I don't know how the split timeline/Hyrule flooding created in Wind Waker will ultimately connect to the older, chronologically-later Zelda games. It could be that a whole new Hyrule had to be created in wake of the flood and that, therefore, everything is technologically rebooted, explaining why there is less technology in the future of the Zelda universe. I don't know. But I still think trains in the Zelda universe is weird.