Instead of going through Mail 2's Import menu, do the following (this applies to those of you that backed up your Library and did a fresh install rather than an Upgrade):
1.) Quit Mail 2 if it's running.
2.) Remove the Mail folder from ~\Library (if it exists)
3.) Remove the com.apple.mail.plist from ~\Library\Preferences (if it exists)
4.) Copy your old Mail folder from your backed-up Library to ~\Library
5.) Copy your old mail.plist from your backed-up Library\Preferences to ~\Library\Preferences
Then when you run Mail 2, it will update your old mail and settings properly.
I'm not sure if there are leftover files in the Mail folder that could safely be deleted though after this process...
1.) Quit Mail 2 if it's running.
2.) Remove the Mail folder from ~\Library (if it exists)
3.) Remove the com.apple.mail.plist from ~\Library\Preferences (if it exists)
4.) Copy your old Mail folder from your backed-up Library to ~\Library
5.) Copy your old mail.plist from your backed-up Library\Preferences to ~\Library\Preferences
Then when you run Mail 2, it will update your old mail and settings properly.
I'm not sure if there are leftover files in the Mail folder that could safely be deleted though after this process...