This is a slightly old post but having read it I was wondering, was your duplicate problem caused by Thunderbird; Mail or something else.
I am considering moving away from Mail to Thunderbird. I had problems with Mail-Act-On creating duplicate e-mails and not sending them to the correct folder.
As for IMAP, not all of my email providers support IMAP. For example O2, who for a time were the sole supplier for iPhones in the UK. Apple obviously didn't care whether O2 supported IMAP. I don't have an iPhone myself but I do have an iPod Touch.