Looking at:
>>> import pwb, pywikibot as py
>>> s1 = py.Site('test', 'wikipedia')
>>> s2 = py.Site('test', 'test')
WARNING: C:\Python27\lib\importlib\__init__.py:37: DeprecationWarning: test_family is deprecated for 6 days; use wikipedia_family instead.
__import__(name)
>>> s1, s2
(APISite("test", "wikipedia"), APISite("test", "test"))
>>> s1 == s2
False
>>>either the comparison should return True or py.Site('test', 'test') should redirect to a site object giving APISite("test", "wikipedia").