Looks like the folks at Mendeley have been quietly making some big improvements.
When I first started using Mendeley, I decided to drag a folder of one hundred or so PDFs into it, since it could extract the bibliographic metadata from PDFs. The consequences were disastrous, with a dozen documents named "Society" and all published in "Science". Overall, less than half were correctly imported, and many entries were unrecognizable.
Since then, I don't drag PDFs into Mendeley. This means that bringing in a new document requires a few steps: get the metadata from a journal webpage (automatically using a bookmarklet), download the PDF, and finally associate the PDF to the document.
Today, by accident, I happened to drag a PDF into Mendeley. To my surprise, it was imported perfectly, with all bibliographic data correct. I decided to try another. And a few more. All came in perfectly. I also found that dragging a PDF of a paper already in my library DID NOT create a duplicate.
Thanks, Mendeley developers. Please keep it up.