I have found http://digitalhominid.apesseekingknowledge.net/?q=node/5 a method allowing you to slim down your Mail2 folder to the size it was before upgrading to Tiger.
I have tested it and it works fine, not a glitch and my ~/Library/Mail folder went from 200MB to 100MB, juste like it was under Panther/Mail1
The trick: erasing the Mail 1.x format mailboxes and indexes that Mail 2 DOES NOT DELETE when it converts your mailboxes to the Mail2 format (individual file for each email vs one file per mailbox in Mail 1.x)
[moose: I tried it too and I was healed and now the girls love me and I drive a Ferrari. Well, ok, not exactly but it did work without a problem].
