I thought Phantom Hourglass was one of the worst Zelda's I've played. Not bad, but not what I want from a Zelda game. If the game has good dungeons and exploration, though, I'm good.
I think I'm near the end of Spirit Tacks by now, and I'd say it is better than Phantom Hourglass, but still the second worst Zelda game. The dungeons and puzzles are much better than Phantom Hourglass' and it's a shame that you won't spend most of your time doing that stuff. The overworld in Spirit Tracks takes up more time than overworlds in any other zelda game. It is by-far the worst thing ever in a Zelda game and one of the worst overworlds ever. Phantom Hourglass let you move in every direction slowly. Spirit Tracks has you moving even slower on fixed tracks and it isn't until near the end of the game when more convenient tracks pop up to make the travels a bit less suicidal.
What's worse is that every side quest in the game deals with unlocking those extra tracks, and all are essentially "drive guy to place, watch for railway signs / transport items to place / catch rabbits as you ride around". The majority of the game for me has been spent at my computer or watching TV as I occasionally glance at my DS and tap to kill a baddie as I wait another couple minutes to arrive at my destination. The best is that there are warp points, right, but they're in placed in the worst locations. Using any warp point still takes a couple minutes to go where you need to be.
Other problems are the flute rhythm sections, which involves dragging around a flute on the bottom of the screen as you blow into the DS mic, and the the general tone of the game. Where Phantom Hourglass was influenced by Pirates of the Caribbean, Spirit Tracks seems to be influenced by animu. Part is FullMetal Alchemist in how the main dungeon you visit is about Link interacting with Zelda's spirit bound to an armored suit while the general tone is moe / uguu behavior from Zelda. That stuff is mostly avoidable thought still weird.
But yeah, the dungeons and puzzles are way better than Phantom Hourglass. If you ever had trouble dealing with the overworld in other Zelda games, this is about 1,000-times worse. For me the dungeons and puzzles are good enough that they save it from being as bad as Phantom Hourglass.