Apple Users

I did a clean install of Yosemite last year. But with El Capitan I just did an 'upgrade.'

I didn't have to enable iCloud Mail, but my iCloud folders were hidden and I had to click 'Show.' Gave me a start for a moment, but the folders were on my iPhone, so I knew they were somewhere.

I had Photos set to not start when my iPhone was attached in Yosemite, but it reversed the setting for some reason. Toggled it. No big deal.

My USB DAC won't work at all. Seems like this is a known issue and my guess is that Apple will fix this soon. Audiophiles are not happy about this.

This explains the Repair Permissions thing:
http://www.imore.com/say-goodbye-repairing-file-permissions-el-capitan

Dunno about the bookmarks thing. I know you can now 'pin' bookmarks at the top of Safari. It gives you a mini-tab with the first letter of the site (interesting, but not particularly helpful, imo). That's not what you are seeing is it?

Otherwise it's very solid. Overall, this is the cleanest upgrade I've ever done. Really built on the bones of Yosemite.