I agree with you in part about the over world.
For me it’s the only section of Spirit Tracks that’s disappointing. It really is anti exploration – even the boat let you draw your own path. But the game has some of the hardest (and most fun) Zelda boss battles to date and the dungeons are some of the hardest in years.
Plus I thought the story was well presented and the tracks themselves were tied in cleverly. On the graphics... well I've never been a fan of the cell shaded style on DS - it just looks wrong to me. I'd rather go back to 2D, but you can't have everything.
I just hope Zelda Wii brings back over world exploration on foot… if there is one at all.