Samsung S4 mini 4.2.2, I just turned off the system update in android settings->More->System Update on the phone. For Apps, I had to go to play store while on the phone (not through computer), click the three bars, then settings, then Auto Updates, Select Do not auto update apps. It is very easy to update apps individually later. I only update apps after seeing what changes have been made. If an app is working to my liking, I don't update because most likely the app functionality will be reduced, changed or broken in a subsequent update in my experience.
There appeared to be some bugs early on because all of my apps tried to update at once (like 30 apps) on two or three occasions but since then it has worked fine. My system has never tried to update. From my understanding, you can backup the apps (downloaded only, not system) using something like Kies to a computer. You can then reinstall that app backup should you have a problem with a newer version. However, there is no specific version history of apps on the play store that I know of so it is up to you to keep a backup. Also, my understanding is that the System Update is permanent (i.e. you can't go backwards) without rooting your phone. So if you system update and don't like it, too bad.
However, that being said, Google Play Services appeared to update just the other day without intervention even though I had these settings turned off. If anyone knows how to stop this, it would be appreciated. It appears that the update has now killed my battery life. I am now in a search to hunt down how this happened. Of course, I can only uninstall Play Services back to the originally installed version, not the previous version so I am kinda screwed.
I don't understand why google does this as a company, stealthy install stuff without our knowledge? This is my number one pet peeve. They don't even provide notification. I don't understand how anyone in their right mind could think auto updating without user knowledge is ethical. Its one thing for me to turn on auto updates and then for them to change stuff, but when I clearly and specifically turn off auto updates and they still do it?