If you are thinking about replacing or painting the panels just because they are fading, try using a heat gun first. I have an 04 so I haven't tried this on my 4Runner, but whei bought my Jeep the fenders were white and chalky.
Hitting them with a heat gun brought the color back right away, it is amazing and they look brand new. It also takes out minor scratches.
Make sure you get a heat gun, not a hair dryer. They are only like $20 from walmart in the paint section.
Good luck