ScreenOS is an aquisition of Juniper that has a longer history as a firewall feature set. As a result there are a number of features and functions that ScreenOS has that are not yet in JUNOS. The operative word is "yet". The intention is for JUNOS to replace ScreenOS on all platforms down the road.
For my use in enterprise networks the main sets of features we still need ScreenOS for are IPSEC VPN advanced features. Things like auto-complete VPN on hub and spoke networks. And if you look at the concepts and examples guide you will see many more VPN based setups that are either more difficult or not possible in JUNOS just yet.
So in general, see if your network design will work in JUNOS and use that if it does. But ScreenOS will be there and supported for those of us that need other features for the full life of our equipment. These previous posts discuss the transition plans:
Roadmap
ScreenOS EOL?