I’ve seen too many neons missing a few sqaure feet of paint, although my wifes (an '02) is fine. Honda is not necessarily know for bad paint, but the clear coat they used in the 80’s and 90’s was know to fail prematurely. As for the dealership, the are doing exactly the opposite of customer service. Have you tried to speak to management? Try and get to the GM, not the “service manager” which are basically useless in these situations.
Also, try calling Honda themselves. Explain what is going on, and how the dealship is treating you. I have seens this done quite a few times and usually Honda will step in and force them to do what you want. My buddy with an 03 Si had dash issues, and after the dealership screwed up a few times and gave him the runaround, he called Honda and they took care of everything. Try it and keep us posted.