I have a long history in the software business, including starting firms. I can tell you that as CEO, I paid extremely close attention to all trouble reports and every bit of feedback from our customers. Customers are the ones who pay the bills.
I also can say as person with deep experience development, there is no evidence right now concerning what is causing the problems we have seen. I think it is more likely that there is a problem in the El Capitan boot sequence. I say this; because what we are seeing occurs immediately after the chimes have confimed that the CPU, etc., are working correctly. Once that happens, I am betting that the boot sequence, probably the kernel, should be looking for the boot drive and then attempt to mount it. That is where the sequence seems to be failing on my machine. The boot drive seems not to be mounted.
It is absolutely inconceivable that Apple would allow any third party app to interrupt the boot sequence of any version of OS X. Inconceivable. This issue is computer manufacturer 101. For example, the BIOS on PCs used to take care of this. Except for the clone BIOS developers, no one had access to the BIOS. Same was true of VAX/VMS systems. Without bulletproof integrity in the boot sequence, it would be impossible to put products out in the market with any assurance that they would perform in a predictable way.
On this issue, I tried everything I could on my machine to eliminate any possibility that something I had hooked up to the machine was a potential problem. USB devices at the top of the list. Furthermore, it is very strange that the no boot problem would come in from the blue when I had run for two weeks with no problems. During that time, I made no changes to any of the installed apps. None. It also is curious that the failures we have seen do not generate an automatic trouble report to Apple. I know they don't; because I turned off my routers. No way for my machine to send or receive anything.
Next, I have several virus and malware detection apps. Dr. Web, ClamXvs. I run these diagnostics every couple of days. I also keep very tight control over cookies and databases being created by my three browsers, Safari, Chrome and Firefox. And I use Drive Genius to monitor the condition of my drive. In other words I my machine as pristine as I can. In reviewing the logs, I can see no issues detected by any of these diagnostics in the days leading up to the boot failure.
Finally, once I returned to Yosemite with exactly the same apps, everything went away. The boot sequence saw the drive perfectly, just as it should.
In conclusion, let me say as a veteran of the business that problems such as those we are seeing are not evil spirits in the hardware or software. There is an engineering explanation. Apple is the one that needs to find it. They need to audit their own code, particularly looking for ALL changes from Yosemite that in El Capitan. Same goes for auditing the interfaces to hardware, particularly the models of machines that have been reporting boot problems.
Once again, customers rule. Companies ignore what customers say at their peril.
All of this said, I began using Apple computers starting with the Ii c. There have been incredible few problems over the years. The conversion to Unix based OS X was amazing, and all that has happened since is easily the most significant technical achievement in the history of computers.
No way I would use anything but a Mac. I hope they get this El Capitan boot problem fixed asap and not resort to finger pointing base on no hard data.