My problem with Mail on Yosemite has been the same on three different Macs; new iMac with Retina display, new MacBook Pro with Retina display, and older iMac. Same issue. Half the time or more Mail freezes up upon launch, which required a Force Quit. Upon restarting, most of the time Mail would function OK, but occasionally hang again, always with the same error-- Application Not Responding. I've tried every fix on this thread and other website threads to get it fixed with nothing working.
Here's what I did to fix it.
I left the Mail Preferences window open to Accounts. That's it. Now, when I restart the Mac or it starts up automatically in the AM, Mail launches as per normal, but with the Preferences window open to Accounts. No problems since. None. Zero.
I have over a dozen email accounts, all IMAP, ranging from Apple's iCloud to Gmail to standard IMAP accounts, personal and business. Obviously, there's a bug somewhere. I came upon the fix by disabling all email accounts, re-enabling each, one-by-one, then doing a shutdown and startup. About five re-boots in I inadvertently left the Preferences window open to Accounts. No freeze on the next reboot. When I close Preferences, the freeze begins again.
It's a cheap fix but it took a long time to get to it.