I am also experiencing the same, but with mild lowering springs (H&R OE Sport, 0.75" drop on 2006-07 cars, 0.20" on 2008+)
I owned a 2012 GTI prior to this, and that car was much softer than the 2007. I don't remember the stock 2007 having such a bumpy ride, but I do remember that the bumps felt...