Jim:
If I had the choice, I'd rather work with a properly set up CMS for optimization, because you can structure documents so that they're optimized by the template.
For example, if you can translate a page topic into the <TITLE> and initial heading, force users to input section headings, etc. you end up with a lot of optimized content without having to tweak each page.
The biggest mistake I've seen is redirecting from
www.domain.### to something like
www.domain.###/default.asp, and that kind of thing that can prevent the site from getting crawled.