yabut…
Like several posters (including myself) stated, it’s not actually faded and anyone purchasing it will immediately see that it is part of the color scheme and that the kayak really is in good shape. It’s unfortunate that you are not happy with the color pattern on your kayak but it will have no negative effect on its resale value so I wouldn’t worry about it. 
You are in luck.
Most people don’t look at things the way you do. I know the boat and have never thought it looked faded. Obviously it was someone unfamiliar with the coloring process who commented on it. Also, why are you worrying about it now. It may get cut in half by a jetski before next year. Wasn’t this one supposed to last more than a year? LOL. I am already scouting out my next one as well.
Unfortunate happenings
The local shop carries a huge selection of Dagger, Perception, and WS yaks in all colors just for that reason. Percepton and Dagger have it together when it comes to roto mixing colors and I’ve seen some fantastic looking effects. Boats that don’t look so hot are picked up as blems at a reduced price…nothing wrong at all with the boats except the way they look. Typically you can save as much a 100 bucks on a new boat if you don’t mind how it looks.
It’s unfortunate that this was an ordered boat because they can not guatantee the color mix results as the boat is formed in the rotating mold.
If you really hate it take some photos and email them to Wilderness System. I can’t tell from that one photo but if it’s really that ugly they may be willing to send the supplier a new boat for you. It would have to be one “ugly baby” though before they take it back!
Wilderness Systems make a fine solid color yak but they just don’t seem to have the experience that the other companies have when it comes to blending color.
We should have a Paddling Net photo contest to see who has the badest a$$ color mix on a plastic boat…Here is a Dagger Zydeco I once owned.
http://community.webshots.com/photo/101380837/398513497scnhAu
used to be real fashionable…
Mixing various colored pellets to come up with strange colored kayaks was all the rage for quite some time (especially in whitewater kayaks). Now most whitewater kayaks tend to come in solid colors or slight fades. I think there were concerns raised (valid or not) that the multi-colored kayaks like the one you linked were weaker than the solid colors.