Well, I thought the train gave enough of an open feel in Spirit Tracks, especially when you could open new tracks with the force gems. The boat is a different matter, because I don't really see a need to let you get off when you want. Those are just my opinions, though.
I mean, I did misss the ability to get off the vehicle in Wind Waker, but in the long run, I don't really see how Phantom Hourglass could have improved because of it. I was convinced that the reason people didn't like PH was because of the repetition and the comparatively bland soundtrack (which are complaints I happen to agree with) but I actually liked the way the game handled the boat travel. I thought it fit better for a portable feel, even though I can see many finding the sailing tedious just like with WW. (that's probably to be expected)
As for Spirit Tracks, I don't know why that one is claimed by some people to be regarded lowly. My guess is that it's because of how similar it was to PH, like a corrected version of sorts. Maybe that description doesn't give it enough credit, though, as it did a lot differently. It could have also been because of the train, which I didn't mind, but that's just me.
That said, if future portable games had more open overworlds, that would most likely be a good thing, I think.