I've got a clone of my El Cap install, Backblaze and a Time Machine backup. Juuuuust in case.
So far the upgrade:
- nuked my desktop folders (lost in the iClouds). Restored the files from Backblaze.
- blew up my Photos library thanks to some sort of DB error. It rebuilt it and then regenerated 21,075 thumbnails (the photos were still there).
- broke Safari Extensions including 1Password, Buffer and Ghostery. They look to be deleted, but aren't. I periodically have to drag them back up to the toolbar to get things working again.
- broke SMTP for my work mail. There's some new thing to "manage connections automatically" that doesn't. Fiddled around and overrode that so I could put them in manually and it all works fine now.