I own a blue Stryker and I have had the same problem with mine. I have gone to other dealers in the area and they all had the same problem. Even the copper and black ones. A Yamaha rep looked at the bike that I wanted to buy and stated that it was "Within Factory Standards". They did not want replace the fenders. My dealer used some 3M body shop compound and hand rubbed the paint. It looked much better, hence, I bought the bike. I went and bought the same compound and I have done it over one more time and it still has improved it more. I will do it again once I get more time. I can post tonight what the 3M product is.
Overall, though this has been a very negative experience for me. I have owned two Kawasaki's before and I have never had a quality issue of any kind. I love my bike, but I am disappointed how Yamaha handled the situation.