How can I get better HVAC airflow?
The fact that one branch duct is at the end doesn't mean much. You could install a damper there to balance flow a bit. 

Of bigger concern is that they used flex duct and bent it severely. If the one in the photo is any indication, they didn't do a great job. You shouldn't see such sharp, tight bends. It also doesn't appear that flex duct was necessary there, but was used to save time (and maybe money).