Should I be using SCUP?

Hi, Need to move into modern times for application deployment, i.e., stop using GPO's, and work smarter.

We have SCCM 2012 installed and working for SCEP but that is about as far as we have gone.

I'm confused as to whether I should be using SCUP or not. Is SCUP is going away? Should I just focus on MSI deployment? Seems most of the blogs I've found for deploying things like Flash and Java use the MSI.

Regarding Flash, I'd really like to start uninstalling(!).

Thanks for any advice.

Bob