I'm in the same boat Kurt, mine is work station computer and nearest apple store is 120 miles away.
The guys commenting above are just going to keep defending El Capitan and tell you it's your hardware or you are crazy though. You know, us crazy Mac people that hate macs.
I had a flawless, fast, awesome, PRODUCTIVE Mac when I had 10.6.8. Nothing changed on my computer. I did the recommended install and it all went to crap. Then after weeks of frustration I wasted an ENTIRE DAY re-installing from scratch and wiping my HD. The same annoyances are still there, and even after 10.11.3. They keep adding more and more crap that no one needs to the OS and then big surprise there are tons of glitches. Yay, my dock and windows are transparent, neat! But it takes me 45 seconds to drag and drop a PDF into a new folder... but my transparent things, so who cares!
YES we are just complaining. I don't get payed to make operating systems or trouble shoot them. You expect a company making billions to provide you with error or minimal error free operating systems.