For those still experiencing the persistent "Welcome to Mail" dialogue after trying the other approaches here, here's something that may help. I tried the disable/re-enable accounts, rebooting, etc., all to no avail. I was not ready to remove all my mail files, start fresh, and drop my local folders back in yet, but I was ok doing one last thing.
In my Mail setup, I had several disabled accounts which I only activated once in a blue moon for testing/whatnot (e.g., my parents email setup to help them if they had trouble, etc.). What I did was flat out deleted these (using the minus [-] button below the accounts in Preferences... | Accounts tab. Granted, I had Mail.app flat out crash on me when I deleted the 2nd one (and I reported that), but when I fired up Mail again, no welcome message, and those accounts were gone. Haven't had the welcome message since.
I suspect Mail was seeing something in those accounts (since they were never active after the upgrade) indicating an old mail structure. Maybe launching Mail after upgrading and doing the "Welcome to Mail" bit to upgrade your mailboxes checks ALL accounts but only upgrades active ones. This would explain the behaviour I was seeing.
Anyway, thought I'd throw that out there. If you have disabled accounts, either delete them if you don't need them, or enable them and quit/start Mail to let it get at them. Then disable them again. Maybe that will help.