If you just want to know which titles of folder 2 (candidates) are already in your base tree and you want to delete/disregard them and just copy/move the rest, grouping (available in premium version) does that job. Automatic tagging in free version is almost unusable for larger collections.
You can rearrange groups by bitrate, length, duration etc., but these are no quality criteria in a strict sense and thus arbitrary from that point of view. I agree that these criteria may be sufficient in many cases, but a 256 kBit MP3 encoding obtained by reencoding a 46 kBit file is worse than a one-step 128 kBit encoding. A file with longer duration is typically less prone to truncation at the beginning or the end at an average, but a file with one second missing in the middle and additional 5 sec silence at the end is definitely not the better one though it's longer.
Adding quality to rearranging criteria is promised for a later version, but to be honest: for critical (e.g. historical) samples I would look into the quality comparison (clipping, spectrum ...) or even listen to both files before I would rely to any automatic criteria to delete one of them.
