Problems importing mails from Yosemite to El Capitan GM

I can see why you would want to start afresh with El Capitan, but there is no clean and easy way to do precisely what you're asking. If the general intention of what you're doing is to start with a clean system, but reliably transfer over your user account data from Yosemite (including everything in Mail) then you can do that:

Make sure your TM Backup of Yosemite is up-to-date, then open the Migration Assistan app in El Capitan GM and select the Yosemite TM backup. Deselect everything but your user account and allow it to migrate it over.

This is as clean and simple as it gets for the scenario you're describing, but there is one caveat - you'll already have a new user account on El Capitan so make sure that it doesn't have the same name as the one you are migrating. Give your migrated account admin rights from System Preferences > Users & Groups (if it hasn't already got it) and you will be able to delete that account once you've logged into the migrated one.

-Max

Hey, In my case the import time kept increasing while stuck on a specific folder. I checked the folder and it turns out my mail was trying to import a 24GB folder mail. So I deleted it, tried the importation again and it worked. That folder is in the Library/Mail/V2 or V3 section.

Hope it works