Hush

Another character who could benefit from the longtime friendship between Affleck and Damon would be Hush. And he is not a superhero. A childhood friend of Bruce Wayne, Thomas Elliot played strategy games with Bruce, teaching him how to think like his enemies. And this came in handy when Bruce became the Dark Knight.
Eventually, holding a grudge against Bruce for inheriting the entire fortune of his family, Thomas killed his parents and started travelling. But, in the end, he returned to Gotham, with the purpose of killing Bruce Wayne. With the help of Riddler, he also found out who Batman actually was.
In such a role, Matt Damon wouldn't use his Jason Bourne skills too much. However, as he has proved many times, he does have the acting chops needed for a superhero thriller. If Ben Affleck also directs him, it would be perfect.
In this way, Affleck will not have kept the best role for him.