As for the ratings in the store, I'm fairly convinced that there is a large cadre of people out there who just give Apple bad reviews just because. Just as an example, in the online store the ratings for the usb-c digital adapter for the retina Macbook and the usb-c power brick are both at 2 stars. Which is ridiculous. Are those devices perfect? Nope, but they both do the job they claim to do and in the case of the adapter, it's the only adapter that can do what it does available anywhere for any price some 7 months after release. It's just sour grapes.
I don't doubt that people are having issues with El Capitan, but honestly, it is on you to make sure that you don't have any critical incompatibilities before you permanently upgrade a critical machine. You have to do exactly the same with Windows, every time. I would never, ever, upgrade a critical machine on either platform before having a complete, tested backup that I could restore the entire system to in minimal time with minimal effort. I had some early issues with the El Capitan beta on my Macbook but 1) it's not a critical device for me and 2) I had a backup that I used to go back to Yosemite in about an hour while I did something else. No big deal. On my iMac at home I know that the potential for disruption is much higher if something goes wrong and the real benefit to me of upgrading is much smaller, so I've put it off until I have some compelling reason, or have the time to deal with it in a way that I can easily restore if necessary.
Apple has done a pretty good job over the years of making OS X upgrades feel a lot like iOS upgrades, but there is still a lot that can go wrong, and they cannot possibly test every combination of scenarios. There is a reason that business Windows users are usually at least 1 release if not 2 or 3 behind what's current. Microsoft is trying to change that with Windows 10, but it's a big question as to how successful they will be. They are asking for a lot of trust from their users, and so far it hasn't been going well.