From what I've learned, there are a few good reasons. We talked to several geothermal, HVAC consultants and took a couple of classes where they have said the same thing - Metal ducts are better. Metal ductwork lasts longer, is easier to clean, doesn't get particle buildup as easily as flex duct and the air flows better (less possibility for restricted airflow, which causes A/C inefficiency!). A/C usage and inefficiency accounts for a lot of Texan's house bills, so this is pretty darn important. You must insulate the metal ducts on the exterior to keep it from sweating if it's cool air or losing its temperature if it's heat. The only disadvantage I can see besides the expense, is that there have been cases where sound travels through the metal ducts to other parts of the house. There are solutions to fix this (duct liners), but I don't know what that does to the efficiency of the ducts (which will defeat the purpose of the metal ducts!).
The alternative has been to get flexduct (the most common in new homes) or fiberglass ducts (made with a rigid fiberglass duct board). The advantage is that it's way cheaper and already insulated. The problem that occurs is that flexduct bends, restricting airflow and being a lot more inefficient. They can also bust open (some guy found a little rat's family home in one once!EWWWWWW) if little critters can get in, and they are difficult to clean. 
Also, you will want to clean your ducts periodically, as there is always a danger of getting fiberglass particles, mold or dust in the ductwork. You do NOT want to breath fiberglass, as that is super dangerous to your lungs, which is why you always need a mask when putting in batt (fiberglass) insulation. With metal ducts, it is easier to clean very thoroughly with a brush. Another tip is that if you are sealing your ducts, always use MASTIC tape not DUCT tape, as mastic tape is better quality and does not wear out as easily as duct tape.
Metal ductwork will cost us about $4,000-5,000 more than using flexduct or fiberglass. But again, my husband says it's worth it! (*sigh*). I guess we're going to have to wait a little longer to get another car :-).














