Pixel Desktop stops responding after updating Pi3

[OsenisBombastis]

After I update my Raspberry Pi 3 software to the latest version using apt-get update, then apt-get upgrade, everything stops responding in the Pixel Desktop. Keyboard, mouse and wi-fi ALL stop working. I've been avoiding the updates for months, since this has been a persistent problem. Every time I do the update, I end up reinstalling the OS from the image and keeping it un-updated. Luckily I have installed RetroPie with the OS, which forces it to tty1, where I CAN use my keyboard. Though wi-fi still doesn't work (plugging in a network cable allows the network to work). I've even updated the firmware, just in case that was the issue. It's still a no go. Am I the only one experiencing this issue?

[vinaypundith]

Try rpi-update before apt-get upgrade, just in case the new versions of programs installed by apt-get upgrade need a newer kernel version to work.
What do you mean by "I've updated the firmware"?

[fruitoftheloom]

After I update my Raspberry Pi 3 software to the latest version using apt-get update, then apt-get upgrade, everything stops responding in the Pixel Desktop. Keyboard, mouse and wi-fi ALL stop working. I've been avoiding the updates for months, since this has been a persistent problem. Every time I do the update, I end up reinstalling the OS from the image and keeping it un-updated. Luckily I have installed RetroPie with the OS, which forces it to tty1, where I CAN use my keyboard. Though wi-fi still doesn't work (plugging in a network cable allows the network to work). I've even updated the firmware, just in case that was the issue. It's still a no go. Am I the only one experiencing this issue?

Raspbian Wheezy ?
Raspbian Jessie ?
Raspbian Stretch ?

FYI Pixel Desktop was retired July 2017 !