Well I think it depends in part of the type of template. I've broken templates into 3 categories.
1) Their are templates that would be considered more like cookie cutter sites, where every one is almost identical. (Some business opportunities have sites like this.) Search engines don't like them.
2) Then their templates like you find at template monster. Even though people may customize them somewhat MY GUESS is that tons of newbies could be using the same template without doing much to change it. It would not rate a duplicate content penalty or anything, but my guess is G may not like it as much of it has the same footprint as hundreds of other sites.
2 A) Another issue with highly stylized templates like some you find at template monster (for example) is that many are designed for looks and not for SEO so may not rank very well to begin with.
3) There are lots of CSS, HTML and Blog templates that are great for SEO. Some are designed specifically for SEO. But these templates are more just a framework of design elements. Each site designed with one would be pretty unique.
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