Perhaps the Adobe Flash Player will not be around anymore in a few years. Until then, some of us are still using it, people like me. I don’t fancy the update mechanisms it offers, though, neither automatic updates nor the annoying pop-up thing.
There has been some Bash code around since a long time on how to update the Adobe Flash Player from the OS X command line. I have taken some of it and adapted it to current OS X El Capitan. When called, it will check if an update is available and, if it is, install it.