I agree that those are terrible. Box mounted 6x9's? Why? Not to mention you have just created some massive blind spots in your rear view...
I understand that you were probably trying to make it so that they aren't deflecting sound straight up into your back glass, but the look hurts more than whatever sound quality increase you may be receiving. I don't know the stock location of the speakers in the Mk7, but installing the 6x9s to the sides of your rear seat with a modest subwoofer dropped in the rear shelf would go a long way to improving your system's acoustics without taking up space in your sightlines...
You could have at least covered the boxes in a blue material to match the rear shelf...
On the plus side, are those Pioneer Premier's? Not too many people people brag about Pioneer for audio, but their Premier line is very nice sounding. I used to have a set in my convertible. Nice looking speaker set.
Now get them out of the boxes!