It does change depending on how many trains they have going at once. I can't remember which part gets cut out on the short version, but I rode the train a few times a few weeks ago and noticed some major differences depending on the time of day and the number of trains running.
I don't think they'll do away with it altogether until they run out of space to put it. They've already had to push it back to a new location because of TGS. If they put a new coaster back there, who knows what they'll do. It would take a chunk out of the park if they did away with it though, I can't remember ever going to SDC and not being robbed on the train.