I think the main reason is that they are stylistically so different from the originals. I am not a "hater" but I was disappointed with the prequels, particularly TPM, because there was nothing to make me care about the characters. I felt no chemistry between Anakin and Padme so his fall to the Darkside was less believable to me. I thought the novelization of RotS was much better at convincing me that Anakin would do anything to save her. I think the overall story/plot was good, it just wasn't executed as well as it could have been.