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I thought some more about this issue and the current behavior seems 
wrong and potentially dangerous. Consider the following code:
class x: 
 pass 
class y(x): 
 pass 
try: 
 raise y 
except y: 
 print "a" 
except: 
 print "b" 
It prints 'b'. Now, suppose in preparation for 3.0 transition someone 
adds "__metaclass__ = type" to the module with that code. The result: 
it prints 'a'. Since the difference in behavior is in error handling 
code, which in my experience is often not thoroughly tested, the bug 
introduced by a seemingly innocuous move from old to new style classes 
is likely to trigger in the worst possible moment. (For example a wrong 
roll-back logic is applied after a failed database commit.)
My understanding is that the current logic of bypassing the subclass 
check in PyErr_GivenExceptionMatches in the case of new style class 
which is not a subclass of BaseException, is designed to support string 
exceptions. Maybe a better choice would be to exclude only string 
subclasses from a subclass check.
I will submit a patch if others agree that this approach is worth 
considering.