I recently ran Migration Assistant on a 2011 MBP running Mavericks to a brand new, fresh install on a 2013 rMBP and it has completely hosted Apple Mail.
It moved over all of my accounts in the Internet Accounts prefpane, but Mail itself thinks that it has no accounts. So when I launch Mail, it asks me to add an account, and if I hit cancel it quits because it thinks it has no accounts.
If I remove the accounts from the Internet Accounts PrefPane and add them through the Mail interface, the Mail check-box associated with the account gets unchecked.
Best Answer
Turns out I'm not the only person this has happened to. From this Apple Support Community Post, if you quit Mail, uncheck the checkboxes from the Internet Accounts prefpanes for anything Mail related, and then delete the files in the Container folder as mentioned in the posting, everything seems to work.