not unique to newer cars, if you live in a humid environment its been a problem as long as there has been factory A/C. #2's suggestion is how to prevent it, but once mold/mildew has gotten started on the evaporator, its too late.
the way to get rid of the smell is an Ozone Generator. you can rent these from a good tool rental business, or find a detailer who has one. If your favorite detailer doesn't have one, I bet they know who does. this will completely eliminate any organic odors, such as the molds and mildews in your A/C, things like pet smells, baby smells, etc.
basic process is to empty out the car of all your stuff, put the ozone generator on the passenger floor, run an extension cord to the O3 gen, close all the windows and doors, and run it for like 12 hours, unplug it and let car sit until the next day, then open all doors and let it completely air out for 24 hours. O3 is very irritating to your eyes and mucus membranes, so avoid breathing or other exposure.