It's that time of year again, updating OS X. No matter how many times the experienced among us try to warn everyone about steps to take for a good update experience, it never fails people get bit. Not absolving Apple here, even if you take all the precautions, there can still be screw ups. things to consider:
Steps 1 through 5: Make backups before updating. Make backups before updating.Make backups before updating.Make backups before updating.Make backups before updating. Period. Why some people still 'wing it' without backups is beyond me. Some one commented below "Don't trust Apple" after loosing their Mail. Well heck, don't trust anyone, let alone Apple, including yourself. What if you make a human error during the update? Select the wrong partition? What if your power fails, or your hard drive? MAKE BACKUPS.
6) Do a fresh install...don't upgrade an existing working system. run them in parallel until you are sure everything works then switch over. Or clone your existing working system, then update the clone. Honestly, the cost of external drives is so cheap, there is no excuse. By clean, I mean install to an erased/empty partition. this is particularly recommended with El Capitan because of the new System Integrity Protection. If you upgrade an existing Yosemite system, guaranteed there are apps which have littered files all over the hard drive, including folders that are now protected under El Capitan. Doing a fresh install and reinstalling your apps will quickly highlight which apps aren't El Cap ready, and insure you have no junk in your protected folders.
7) If possible don't run the installer from the same partition you are trying to update. Boot from an installer. Instructions everywhere on the Net to make a bootable installer (BTW, doesn't have to be a USB stick, the same instructions work for making a bootable installer on an external drive partition...that's really the way to go, and MUCH FASTER). Installing from a bootable installer and installing to a clean partition, will solve 90 percent of the issues people experience, in my experience, and I have updated A LOT of systems in my day, going back to 10.0.0.
8) Don't update and then find one of your apps isn't compatible. It's crazy how many people just jump right in and update and then discover some app doesn't work. Do your research, or as mentioned above, update a cloned system or do a fresh install, so if something doesn't work, you haven't hosed your everyday system.
9) The last several releases of OS X have had reports of what appears to be a freeze at the very last of the installation, i.e. the progress bar is almost done and appears to no longer move. Now, I'm not saying there aren't cases where it actually is stuck but I've learned after doing many updates that this last step can take awhile. And it varies. One update last night, it sat for nearly 30 minutes at that last step before finally continuing. Be patient. Also that last message that says 'rebooting in a few seconds' or something like that, well, it might be minutes. Be patient.
10) A person in another post said: 'I don't know why the only Apple supported method of upgrading is to download and install over a previous OS. ' No it is not the only method. You can do a fresh install, then use the Migration Assistant to migrate over your data, apps, preferences etc. from another installation. You can either do this during the install, or afterward. I recommend afterward. The migration assistant is located in the Utilities. folder.
Best of luck to y'all ! Unless you really feel you need El Cap right now, consider waiting for 10.11.1 or even 10.11.2. 10.11.1 is already in beta 2 and will be out in a few weeks. Otherwise, try to follow the steps here. Oh, and did I mention, make a backup?