Folks,
I haven't read all the recent updates, but I'm very aware of what the core issue is here. I just wanted to share some real informaton that kind of solved my problem in a way, but doesn't even remotely solve the actual BUG that is in Mail.
As stated in other posts, the problem is related related to either corrupt messsages (or at least "corrupt" in Apple Mail's view), special characters, or some other issue that causes the maibox sync to essentially hang on 1 message. Which may or may not resolve itself, and typically required a full quit of Mail and reopen.
One thing I did about 2 weeks ago was move ALL of my subfolders that were under the Inbox folder to the root of my mailbox (using OWA, not mail!!). As soon as I did that I no longer had any sync issues, in fact I found it extremly annoying because I COULD NOT even reproduce the issue anymore. My understanding is that Mail only actively syncs the Inbox folder, and subfolders, and I think all other folderrs are only refreshed when selected (I could be slightly wrong about this). What this tells me is that some type of message in my inbox subfolders was causing Mail to hang on sync. The even more annoying part is, I tried to move all the subfolders back under the Inbox, and I still couldn't repoduce the issue.
In summary, I moved all the subfolders from under my inbox to the mailbox root, then back, and I haven't had ANY issues with Mail since doing that. Also, I have 2 Exchange account in Mail, both with had this issue and both are resolved after doing this.
While this makes Mail more usable for me now, I am 100% certain that there is still a problem/bug with Apple Mail. This also kind of explains why the Apple engineers can't really get to the root of the problem, because it's so hard to reproduce.
PS, if you want to look at the raw EWS http traffic from Mail, you can launch Mail using this command, which will save MailConnectionLog.txt on the desktop. You can clearly see the problem when examining these logs.
/Applications/Mail.app/Contents/MacOS/Mail -LogHTTPActivity YES -LogMaximumBytes 512 >& ~/Desktop/MailConnectionLog.txt &