If quality is a concern then exporting as PDF is the preferred method.
If you're seeing the opposite you're probably converting to CMYK which would definitely have an effect on the vibrancy of colors.
FWIW, you're the first person I've ever seen report that direct export to JPG as anything more than barely acceptable.
Just thought i might add that i have encountered this same problem and that if i want a high quality jpeg i save as pdf then, open and re-save as jpeg in photoshop.
I never knew my jpeg's weren't top quality until a customer informed that my jpegs were not of as good quality as jpeg's received off other designers they use.
Unfortunately i have no fix for you, but thought it may be of interest to know its not just you!
Thanks to everyone for their respone. I have been dealing with PDFs, Postscripts, EPS, Tiffs and JPEGS since 1996 as a sheetfed & Web Prepress Manager using Quark but now, as a production artist using InDesign for 3 years I find things a little different on the InDesign side and by the way I love InDesign. As I said before thanks for your reponses.