Here's how to fix the folders and other stuff:
- You can fix the folders and just about anything else with XRevert, That's a unique name so it is easy to find it in Google. XRevert can't fix the unearthly blue in the rest of the UI, though.
- The Dock in Yosemite and el Captain has regressed all the way back to 10.4 Tiger. You can bring the Dock back into the modern world with DockMod by SpyreSoft. It doesn't just repair the Dock's appearance, it lets you customize it too.
- You can change any questionable icons in a non-Apple application. Right-click on the old version, show package contents, copy the icons in the Contents/Resources folder, and paste them into the same location in the new application. If you change the icons in applications that require permission to access the internet, you'll need to give them permission every time they launch, but that's not a bad price for esthetics.
I recommend storing the icons on an external drive to repair future downgrades of the UI.
The Hanna Barbera themed versions of OS X, Yosemite and El Captain, need esthetic repair, because they are too flat, they have colors not found in nature, and many of the icons are turning into unintuitive abstract symbols. They all make OS X less usable because it's harder to tell what's what. The UI looks like it was drawn on someone's kitchen table with a ruler and compass by a person with a color vision impairment. Fortunately, Apple hasn't locked us out of repairing it.