This decision is often driven by bore size rather than barrel length. Some say that you should not shoot 3f in anything above a .50. I have heard that you might experience some chamber erosion if using a steady diet of higher charges in .54s. However, some shoot target loads of 3f in .54s without any problem.
If you have a smaller bore than .50, try both and shoot the one that gives the best accuracy. If both are equal, toss a coin.
I think that the only advantage of a long barrel (beyond the fact that I love their look as MusketMan mentions) is in the long sighting plane.
From what I have read, powder did not improve greatly in the years when the long rifles started to shorten.
The barrel lengths began to shorten as people began to roam longer distances over open land and used horses to do this. Long barrels are a nuisance on a horse. I also believe that as sights improved, people realized the long barrel did not really help as much as they had thought and that sufficient accuracy could be had with shorter barrels.
I believe that it was a reaction to the changes in human behavior and an acceptance of a new style. Sort of along the lines of wide lapels and ties vs thin ones.
YMHS,
CrackStock