Some people love flex duct. Some people hate it. Some of us are OK with it if it's done right.
As I've documented here numerous times, many flex duct installations leave a lot to be desired. They sag. They're kinked. They're twisted around pipes.
If there's something bad that can be done with flex duct, someone has done it. And the result of all those mangled flex duct installs is poor air flow, which creates comfort problems, uses more energy, and is one reason systems get oversized.
from Building Science http://www.greenbuildingadvisor.com/articles/dept/building-science/uniform-mechanical-code-looks-limit-flex-duct