You have more than a reason to be annoyed.
I would be asking for some form of compensation, either in the form of a discount (people are getting the free onroads deal from cars ordered months ago that are delivered this month) or with free accessories.
When you do finally get your car, I would be checking specifically for two things.
- damage around the stereo area. Since the MK6 has a shroud that is easy to remove, they will hopefully replace this if it was a stolen stereo.
- damage to the car at all. Check under the car for any signs of overspray or anywhere for paint mismatching. At a friends workshop many years ago the majority of work was coming from brand new cars damaged in transit. At the time it was new Magnas that had been driven off car carriers too quickly and almost ripping off the side sills. If the drivers took more time and chocked the wheels it wouldn't have happened, but they just drove the cars as quick as they could on and off, and any damage wasn't their issue.