Sorry I can't help, I came here to ask essentially the same question. I sync exchange and mobile me, and the handful of contacts that are on both show up twice in my contacts. It's mainly a problem when one of them calls me - the phone says "John or John", and doesn't show the picture that is assigned to him on the Mac. That part is new with 3.0 - it used to assume it was the mobile me one and show the picture.
If your contacts are identical, I'd say don't bother syncing both.