I've encountered the same issue and worked around it by using generic variables that would always be the same for a certain email alert. eg = "System XYZ -source file delay for :"
So a sample subject would then be:
()
Where ENV = DEV/UAT etc.
This functionality allows you to use generic alert templates for all filewait jobs, and just filling in the variables.
A slight problem is that although this works very well, the use of group variables in email / alert actions is (/ wasn't) officially supported by Cisco when I last ran it past then. Cisco, any update in this?