Using a different auth system might be a little complex. Everything is built around the current auth that is in it. I am planning on some additions to the auth system to allow different auth plugins (like Facebook, Twitter, etc) which should help alleviate some of those issues.
The easiest way to integrate would probably be to add a couple of functions to the auth of your choice that use the same name, though checking permissions for apps is done in a pretty specific way, so it could be a pain.
What are the parts of A3M that make you choose that one?