As far as new functions go, I really can't see any way of doing this. To give them completely new functions would imply code changes or new additions.

You can modify the individual stats of the units, but not create anything that didn't exist before.

is is based on assumptions, because you don't really say very much about WHAT you want to add to the agents.

If, for example, you wanted to add some sort of sabotage effect, then that could probably be done. If, however, you wanted to add the ability to kidnap a characters wfie and hold her for ransom.... well... I don't know.

The further away you get from the basic functions of an Agent, the less likely it becomes that you will be able to achieve it.