By the way, I noticed one more problem with Mail in El Capitan:
A few times a day I receive emails that in Mail show up as being exactly the same as the previous email I had received (same sender, Subject, content).
E.g., I receive an email from user@host.com with Subject: "test", which I file to a mailbox.
A while later I get another email that Mail says comes from the same sender user@host.com with the same Subject: "test". Both email have the same contents also.
If I open another client, I see that this is not true, that the second email is from someone else.
I need to use Rebuild a few times in Mail, or delete the directory INBOX.mbox in the ~/Library/Mail/V3 (under the corresponding account path), or restart Mail, or a combination of the above, and eventually Mail gets it right.
Again, I tried today, and this does NOT happen with Yosemite.
I could not find anyone having this same problem in Google, so I suppose I am alone on this one...