Rigid sheet-metal ducts are a far better choice than flexible plastic ducts for efficiency, durability, and health reasons.
Flexible ductwork really reduces airflow because of the turbulence created by the textures and corrugations on the interior of the duct. In many cases, flex-duct is used improperly as a shortcut for tough install conditions; it is twisted and squished in tight spots, creating bottlenecks and flow restrictions.
Proper rigid sheet-metal ductwork is straight and smooth so air flows well. Using 45-degree angles rather than 90-degree-angle connectors on the install will further increase efficiency. It is also very important to properly seal sheet-metal ducts with mastic to prevent air leaks.
Flexible vinyl ductwork rips easily and many types of flex-duct may become permanently squashed if pressure is applied. Flex-duct also degrades under stressful conditions; for this reason, in many states, these types of ducts are not approved for exhaust ducting.
A flexible duct with twists and bends and a rough interior surface will accumulate dust and other particles. Add some moisture to the stew and you have a breeding ground for all kinds of nasty stuff.
You indicate that you are concerned about PVC (polyvinyl chloride, or vinyl). The PVC used in some types of flex-duct does have an environmental impact, but when it comes to indoor air quality, I believe the microbes fostered by flex-duct are more of a concern than the vinyl.