1. I agree with LSchefman said. PRS uses photosensitive pigments to enhance the wood grain and stunning appearance which the brand has been known for for three decades. But this kinda pigments fade out easily over time.
2. Blue Matteo gets faded quickest. See the sample pics I collected from the net below. Each picture consists of
one same guitar shown in before/after its fading. The last one is an ME1 which almost completely faded out.
Other colors with blue pigment in it tend to fade too, no matter how expensive the color charges you, Northern Lights per say. But surprisingly, recently I met a WL McCarty owner finished with Bonnie Pink. Believe me or not, this color also fades slightly after less than 1 year of using. We knew this by unscrewing the pups ring to see the difference of color.
Yes, you can slow down the fading by keep your blue PRS in case when not in use. But to my thought it's
hillarious to keep casing/opening/casing/opening/casing bla bla bla to maintain a $6000 worth guitar to looks as beautiful as the 1st day of possession. I hope PRS addresses this problem seriously.
As far as I see, the colors with least tendency to fade are amber, yellow, tortoise shell, black cherry, emerald green, etc.