Mail.app crashes after update to El Capitan OS
There is a good work around for this, that can be found on the apple discussion forum, here: https://discussions.apple.com/thread/7251820

Should you be in the same position as the author of this, and have multiple mail accounts active, try the following steps:

I had the same problem, but I believe I've fixed it.  It's seems to have been related to the fact that I have multiple email accounts active in the app, as many people do.  The initial download of all messages from all accounts seemed to be overloading the app, causing it to crash.  See if this works for you:


Before opening the Mail app, turn off your wifi connection (prevents mail from trying to download mailboxes from all accounts at once).
Launch Mail app and go to Mail -> Preference -> Accounts tab.
Click each of your accounts on the left side of the Accounts window, then uncheck the box next to "Enable this account."  Disable all of your mail accounts.
Close Preference and close the Mail app.
Relaunch the mail app and reconnect to wifi.
Go back to Mail -> Preferences -> Accounts tab, and enable the first account.  Give the app plenty of time to download all messages until you no longer see "Checking for Mail..." at the bottom left of the app screen (may take a few minutes depending on how many messages you have on the server).
Once the app is no longer "Checking for Mail..." repeat this server for each of your other accounts.  I saved Gmail until last since it's my biggest, which took the longest - about 5 minutes (I use multiple Gmail accounts).


After enabling all accounts, the crash issue stopped for me.  Hope it works for you!