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Thanks for being understanding of the decision. Regarding my comment above about __subclasscheck__ potentially letting you implement this without changing the signature of suppress, here's an example of how you might be able to do that.
First, define a metaclass that delegates type checks to the type itself (similar to abc.ABCMeta):
class FilteredExceptionMeta(type):
 def __subclasscheck__(cls, other):
 return cls.__subclasshook__(other)
 def __instancecheck__(cls, other):
 return cls.__subclasshook__(type(other))
Then, define a factory function to create custom classes based on that metaclass:
def filtered_exc(exc_type, *, unless=()):
 class _FilteredException(metaclass=FilteredExceptionMeta):
 @classmethod
 def __subclasshook__(cls, other):
 return (issubclass(other, exc_type)
 and not issubclass(other, unless))
 return _FilteredException
>>> from contextlib import suppress
>>> selective_filter = suppress(filtered_exc(OSError, unless=FileNotFoundError))
>>> with selective_filter:
... raise OSError("Suppressed")
... 
>>> with selective_filter:
... raise FileNotFoundError("Not suppressed")
... 
Traceback (most recent call last):
 File "<stdin>", line 2, in <module>
FileNotFoundError: Not suppressed
This works because suppress() calls issubclass() explicitly, unlike the current implementation of except clause processing.