I myself don't mind the controls for PH/ST... that is until the other day when half my right hand fell asleep while playing ST.
So anyways, to those not sure on getting Spirit Tracks, I'll say this: If you didn't like PH, you definitely won't like ST. While some things have been improved (especially the music), it's still overall a "blah" experience. It's also very easy like the previous one. So far, the only real challenge I've had is avoiding the one-hit-kill trains, but it's only a problem because your own train goes too bloody slow. Another thing, the train feels like a step down from the boat; it feels much more strict and repititive. Collecting parts for your vehicle is also back, this time you get them by trading treasures with Linebeck. Some other minor changes include being able to keep all the mail you recieved, and being able to roll by double-tapping now. One thing that's much been improved though, is this game's equivilant of the Temple of Ocean King. Safe zones are back and all that crap, however there is of course no timer this time. You can also co ntrol Phantoms by hitting them in the back after collecting Tears of Light. As also mentioned before, you can skip floors you've cleared now.
Oh and:
The Ganon Train seems to have no major importance to the plot from what I've played so far. Also, the Demon King isn't Ganon either; his name is Malladus