I think the wavy lines are due to the fact that 
the think plastic of the bag tends to contract 
easily with even slight temperature fluctuations. 
Where the acetate is clear, the bag moves 
smoothly as it expands and contracts, but where 
there is sticky cel paint the friction causes the 
plastic to stretch slightly out of shape with the 
rest of the bag.  I wouldn't worry about it.  
Either buy thicker bags or replace the thinner 
bags from time to time if it bothers you.   If 
the waviness is showing up very quickly, you 
might want to check to see that wherever you're 
keeping your cels isn't too near an intermittent 
heat source, such as a shelf over a TV set or 
near a heater vent.

As for the line fading on cels that are in open-
ended bags, I have *very* definite opinions on 
that topic.  There is absolutely no doubt in my 
mind that air-circulation contributes to line 
fading.  

For the past 10 years, I've collected cels from 
Urusei Yatura, a series from the 80's, so I've 
had some time to see how well the various bagging 
methods protect a cel.  Cels kept in open-ended 
bags (or no bag at all) fade quicker than those 
sealed up in closed bags.  

In fact, the best-preserved UY cels I've 
purchased were ones that had gotten hopelessly 
stuck to Saran wrap (or whatever plastic food 
wrap they use in Japan).  I trimmed the plastic 
wrap from the back as best I could around the 
edges of the characters, but the wrap is 
permanently stuck to the paint itself.  
Nevertheless, those particular cels have the most 
unfaded lines of any cels in my UY collection, 
despite being nearly 20 years old now.

Just my 2 cents on the matter.