I hope trains make a return in some form or another.
On the handhelds, I see it coming to return in a similar fashion to ST. I never had a problem with way it was set up, just make it a tad bit faster for the high speed and it'll be perfect.
I don't see it in the same fashion for the consoles, though. If we're using some form of transportation, it'll most likely be Epona, she's still the best generally speaking. But I hope they make a train as a dungeon. I really enjoy the totally oddball dungeons like the Snow Mansion, and the Sand Ship has proven that a mobile dungeon can work, so if we can have one of the dungeons be a monstrous train (maybe the Demon Train???) where it's actually traveling to certain locations as we're inside of it, that'll be dope.