I would not like to see the train again, but I'd rather have that than a boat to be honest. The train is set on tracks, meaning it's going to be rather linear. I hate following preset paths as you might be able to tell, so I hate the train.
All the hate being said, I do have to say this: I don't expect we'll see the train again any time soon. Spirit Tracks was panned BECAUSE OF the tain, because of the leap in technology (well, there are a bunch factors but among the fans, most of them panned ST due to trains existing). Nintendo loves to play it safe in some areas while exploring others, so I think they will ditch the train for a while. Perhaps it'll return in a future installment, just not in the near future?