Think 20 years into the future, you need a furnace changed out and the installer tells you that your foundation had filled with water before and the ductwork has all rotted out.! I suggest that you think about more than just duct work efficiency. THink about 10-20 years from now and what the conditions may be then. I myself would never have ductowrk in the crawl space because I have changed out countless systems that have rotted out, its harder to replace and hey more prone to critter damage. I ran across one just yesterday where the foundation had filled with water over the years, and in less than 15 years the entire system needed relacement.

I would make sure all duct work is through interior walls. I have an older house and the ducts to the second floor run up exterior walls. Nothing like having that first blast of cold air when the furnace kicks in to wake you in the morning. Plus I'm spending money to heat the great outdoors as the heat flows out the uninsulated siding.