mail.appmojave
After I updated my Mac to Mojave, the mail app became very slow, particularly with the rules.
I have rebuilt mailbox, restarted Mac and Mail multiple times.
My account connects to MS Exchange.
It takes ages to open rules, scroll down and add new senders to a rule I have created to mark "spam" and move all emails from this sender to junk folder. I have checked today, and to run the rule on one email takes about 1 minute. Any ideas?
Sounds like your Mail preferences are not saved.
Try this (it is not same as using Disk Utility to repair permissions)
You can use the ACL tool on the Recovery HD to do this:
- Boot into the Recovery HD using ⌘R.
- Run
resetpasswordin Terminal (available from Utilities → Terminal).- Select your account from the drop-down list.
- Click the Reset button for Reset Home Directory Permissions and ACLs.
Source: grgarside — https://apple.stackexchange.com/a/110346/
If you are not comfortable doing it above way, there is a application called OnyX that will do it for you (and much more).
E-mails that have been placed into the spam folder by Apple Mail will have this header: 
If you see an e-mail in your spam folder that lacks this header, than the e-mail has been automatically been placed into the spam folder by your mail provider. You should mark it as "not spam" from within your mail service's web client.
Best Answer
I've had the same issue for Mojave and now Catalina. I've posted several 'suggestions' to Apple for improvements, especially the clunky UI, but nothing's come through yet!
The only way I know to speed things up is to move to a new, identical rule once the number of conditions grows to over 100, otherwise the interface just gums up.