I don't know if your trip is long enough to pull this one off, but there are some interesting trains in Eastern Hokkaido. The one that comes to mind is the Norokko-go out of Kushiro--this used to be an old steam train, although I think that ended a few years ago and now it's normal stock. But the train takes a slow trip through the Kushiro marsh, which is beautiful. And if you'll be there at the end of the year, it'll be crane season (you won't be able to see them from the train, but there are several places that can arrange a trip by car to see them).

I think there's something similar between Furano and Biei, but that might be only in the summer.

It's a bit off the beaten track, but well worth the effort if you have the time and like riding trains (The trip out to Kushiro can also be quite nice on a combination of Shinkansen, Kaisoku and locals).

K