For A/C systems this is superior since the cold air wants to fall and this helps avoid stratification. In heating just the opposite is true the hot air wants to stay near the ceiling and stratification gets to be an issue. A ceiling fan on low speed in each of the rooms will improve comfort. The reason ducts were probably done this way was the contractor was unable to run his ductwork unobstructed or if he did he might have compromised the structural integrity of your new home. Plus it was easier to work in the wide open attic. Be sure the attic ductwork is insulated and sealed because you could lose a great deal of your conditioned air to the attic which you don't want.