Phantom Hourglass was probably the worst mainline Zelda imo, and it all had to do with the overly simplistic hand-holding dungeoning. It's like they put everything into crafting this amazing interface (that actually works!) and just dialed in the rest.
Spirit Tracks is better in about every regard, but I have to agree that I'm tired of the vehicle based overworld. I'd kill for a DS Zelda using this engine with an oldschool overworld to manually traverse and explore.