Sorry but android is the new windows. I'm sure you've experienced same or worse on Microsoft's OS and here I've seen the same.
For now I keep my app's and their activation codes on a small cheat sheet so I can start over fresh. There are better backup systems but after being burned by such I went old school and my own way.
my s3 had problems with a google error, and because of that i couldnt use play store.
so i made a back up of everything, and did a fabric reset.
after i turned on my phone, i recovered the back up on my phone.
and it seems like not everything is stored back. my background and the apps on my home screen, the widgets i had nothing of that came back.
also the back up says it backed up 44 app data from my apps. but it only downloaded the apps i had, and when i open them i have to reconfigure en personalize ALL them. its like you download them for the first time. i lost my conversations on whatsapp, my progress with games, my settings in each of them
it also says it would back up my settings preferences. and also my settings are like the first time you start your phone
it did not even back up my sychronisation acocunts like samsung google dropbox facebook etc.
i thought it would be like when you upgrade your firmware, and all remains the same. but now i lost many important things
i redid the back up a few times and also did a fabric reset again and backed it up again nothing helped
sorry for my bad english
my s3 has android 4.1.2
and kies 18.104.22.16823_2