No, the Mail program doesn't have a fatal flaw (though it does have plenty of small irritating features) - there is something wrong with your installation or configuration.
1) run disk utility and perform a disk repair (not repair permissions). Since you have Mt Lion it would be most convenient to reboot into recovery mode (command r on startup) and run disk utilty there. Disk Utility cannot repair the startup volume which is why you should restart in recovery mode. This will ensure your problem isn't a had directory.
2) create a new user account and configure Mail for at least one email account (assuming you have more). Make sure it is one that locks up. If the problem doesn't exists on the new account your problem exists in the account you use. If so, do you use any mail plugins?
3) If the problem exists in the new account start Console and look for errors involving Mail. Do you see any hints there? Don't post all the error messages but feel free to post any that mention Mail specifically.
I'm afraid I have taken the easy way out and moved to Thunderbird.
I have seen several discussions on this subject and the majority seem to feel the product is weak and Apple support either can't fix it or bury their heads in the sand.
It is so totally random that I'm doubtful it's a configuration problem. It has been like it from day one as a brand new machine. I have been an it professional for 30 years and don't recall ever having such problems with a mail client ( I've used Notes, Outlook and sevral linux varieties ).
It's always ironic that I cna have the mail open on my iMac and while my iPad is pinging away in the same room receiving mails the iMac mail is dead.
Thank you for your help and sorry for the rant.