I'm not sure what the base class(es) actually buys us. We could just as well say by fiat that the interpreter will set the traceback attribute of an exception instance to the traceback. Why do we need a special base class to accomplish that? This is Python. You don't need to do isinstance(). You just need to see if it has the right attributes.
Fair enough, though having a common base class makes it easier to augment the functionality -- every exception class would automatically inherit any functionality provided by the base class. But here's the real reason (which I brought up when we had this discussion a few weeks ago but didn't remember completely last night): once we reach the nirvana where all exceptions derive from Exception, we can declare that except: is equivament to except Exception: and then, when we also store the traceback on the exception object, we can (eventually) get rid of sys.exc_info().
BTW, what is the signature for Exception.__init__()? I've written many exception classes, often subclasses of some other exception, but I've hardly ever paid attention to the superclass __init__(). It usually suffices to set the right attributes.
It's been a documented recommended practice to inherit from Exception since the introduction of class exceptions. Why are you suddenly fighting this? --Guido van Rossum (home page: http://www.python.org/~guido/)