Mail is slow to load messages from Gmail, Exchange and inbox.

I have three email accounts in Mail, iCloud (12k), Gmail (57k) and Exchange (31k).  I have just around 100,000 total inbox and sent messages. 
Often, like 99% of the time, I'll get an email alert in notification center and when I click on it mail is unable to display this message because it hasn't come through yet.  Sometimes I'll be looking in Inbox (all three accounts combined) and the message that just came through, or the last dozen messages, aren't there.  If I go to the individual account, I can read the messages that came through.  Other times, inbox is just empty for a few minutes. 
I've given up on using the UNREAD smart mailbox because I'll be reading a message in there and it just disappears because I guess after viewing it for more than 3 seconds means it has been read.
This is growing increasingly frustrating.  Does anyone know of a fix for this?  Do I have too many messages?  I'm really good with keeping a zero inbox and deleting messages I don't need. 
I actually rebuilt my entire computer, erased the hard drive even, just to fix this email issue.  It didn't help at all.

I'm having the same type issue.  I'll hear Mail chime and there will be nothing new. 
I even have rules to make the Dock icon bounce when I receive email from certain people... that will trigger, but no new messages.  Eventually they show up, sometimes hours later, but there was at least one Gmail message that Mail never delivered.  That really has me concerned and looking at alternatives.
All of this started for me after Apple's patch to fix Mail.

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