Well part of it is certainly paper-what kind are you using? I read on Lang's site that his tissue foil models would lose color over time because of the cheap dyes used...
I have personally not had a problem with this-I mostly use money and kami.
Some of my foil models are also losing their colors : my tree frog is slowly going from green to yellow and my purple Raijin is becoming white . Also, the color changes are mostly found on creases. Does someone know why this happens? Since it's only on two models, I assure say that the glue does not have anything to do with it.
Tissue-foil is known to discolor over time. That is one of the reasons it is discouraged by "the pros", even if you can fold it without it wrinkling. The paper uses low-quality, non-acid-free somewhat unstable dyes, and discolors after a while. The glue is also not acid-free
I would say that the best way to have models that will last a long time and still be vibrantly colored is to use the more expensive handmade paper like hanji, gampi, kozo, etc. Since these are usually acid free, and more or less made from all natural products, they presumably last a long time. Tissue paper, as mentioned, and similiar papers tend to be factory made, thus unstable, acidic dyes are used, which cause the paper to fade and leave not so splendid results down the road.