I have to chime in that El Cap has not been "the boss." With the latest 10.11.4 update, I have spurious crashing of Mail and Contacts. Once they crash or become unresponsive, I have to reboot to fix the situation. The one improvement is that the system never shut down with 10.11.3 - it hung on a black screen. The update fixed that. it takes some time, but works now.
Like with everyone else here, the biggest issue all along for me has been Handoff and AirDrop. It is working like clockwork with Yosemite - even if I reboot into it today. 10.11.4 seems to have fixed AirDrop, at least with iOS devices and sometime OS X, but Handoff is only working outbound. Other systems can see my Mac Pro, but there is no inbound Handoff.
Since this is my main desktop machine, inbound is what I need most of the time. Frustrating! I used to fix it by switching Cloudpaird in Coreservices with the Yosemite version, but that does not work with 10.11.4
Bugreports are in and based on some communications, engineering is checking into it.
But I am still waiting for a fix...
I should note that I do not see these issues on my MacBook Pro Retina and my "Continuity patched" mid 2011 Air 11, but they tend to run fewer apps. My Mac Pro has 12 cores and 48GB with about 20TB of disk (spinning and SSD,) so it is my workhorse 24/7 and runs the most complex set of apps.