A general inquiry about what features are LOST when "upgrading" from Yosemite to El Capitan.

For example, the old "MOSAIC" screensaver was dropped somewhere around Mountain Lion's time and has not been brought back.

Any thoughts on what has been dropped (and may be missed) in doing the upgrade from Yosemite to El Cap?

There are old standby troubleshooting procedures such as repairing permissions and logging in as Root that have been removed either because they are no longer needed or because they were vulnerable to exploits. As usual in upgrades some commands and settings have been rearranged or moved, sometimes to non-intuitive locations. For whatever reason some settings seem to be getting lost in the upgrade — they are still available, but they have to be reset. For example I have seen several reports that signatures in Mail are still there but have t be re-associated with the particular email accounts.

I'm using Mail 9.0 and have 2 email accounts, each having its own signature. The respective, account association, for me, did not require any signature re-association between Yosemite and El Capitan.

The ones I have encountered have all had multiple signatures many or most used in more than one account. What that has to do with it is your guess — I have none.

Just noticed one "lost" item :

There is no longer a SECURE EMPTY TRASH option . . . unless by default this feature automatically securely deletes files and folders moved to the Trash.

If not, then a third-party "shredder" will be needed to do the job.

How to securely delete files in OS X 10.11 ‘El Capitan’

Here's something that El Cap added (although most likely something many will not want to activate). ...Auto hide Menu Bar (default setting is Off)

Here's a link to MacObserver about activating Hide Menu Bar

This is something I've wanted because my Desktop (Sys Pref) is set to randomly rotate, every 5 minutes, desktop pictures from my Pictures folder, which has about 100 high resolution, landscape photos (and I periodically update from InterfaceLIFT ). I'm very visual and every since Apple allowed greater control of Desktop views, I've kept my Desktop clear (no files / folders - except my Time Machine icon) since I really want to enjoy a clean view of the high res photos. My MBP is connected to a 24" Cinema Display, which enhances my Desktop view. [I've been auto hiding the Dock for a long time.]

Prior to El Cap, I wanted the ability to get the Menu Bar visually out of the way. ...Now, I can do so. When needed, simply moving the cursor to the top of the display screen, auto shows the Menu Bar, making it easily accessible.

Back in the day when ResEdit existed (especially, OS 9 days), I enjoyed the customization one could do. (It was fun and created a personal identity with one's Mac.) ResEdit's customizing was lost with OS X, but OS X allowed having beautiful pictures rotating periodically on the Desktop, creating a multimedia feel. So now with Auto Hide Menu Bar, I enjoy seeing my desktop pictures without the visual interruption of the Finder.

Thanks for the link to the SECURE DELETE article.

However, the commands do not work as written (i.e. copy/paste).

I remember being able to deeply customize the interface. Being able to modify MBDF resources and other templates allowed you to do some pretty radical redesigns. I recall seeing a good LCARS mod more than once.

But I think in the end, Apple doesn't like it when people do that. They want their product to remain consistent. Though I don't necessarily agree with the result, I can see where they're coming from, from a brand perspective.

I also had Stitch (of Lilo and Stitch) replace my grey startup apple for some time, until Apple closed-source the file that stored the image data. I still miss that...
(I think this was it, there were 2-3 apps that could change it: http://www.howtogeek.com/howto/41091/how-to-customize-your-mac-boot-logo/)

A slight quibble:

It's not the Finder menu bar you're hiding; it's the menu bar, period. The menu bar becomes the Finder menu bar when Finder is the active application, just like it's the Safari menu bar when you're in Safari, etc. But its presence—or absence, if you invoke the Auto Hide function—is persistent across applications.