homepage

The following behavior doesn't make sense, especially since it works correctly for other special attributes:
>>> class F:
	__name__ = "Foo"
>>> F.__name__
'F'
>>> F().__name__
'Foo'
>>> F.__name__ = 'Foo'
>>> F.__name__
'Foo'
Works fine for __module__ and others:
>>> class F:
	__module__ = "mod"
	
>>> F.__module__
'mod'
>>> F
<class mod.F at 0x0212B360>

I don't think this is actually incorrect. Basically setting something in the class body is not equivalent to setting it as an attribute on the class.
This happens with other attributes. Consider
>>> class X:
... __class__ = list
... 
>>> X.__class__
<class 'type'>
>>> X().__class__
<class 'list'>

I think for __class__ it might make sense but for __name__ it seems not intuitive.

Well, what do you expect the name of the class to be? The one you assign __name__ to or the one you pass to type()?

The one in __name__ since logically that happens after the class declaration ('class X' line) and should overwrite the name in the class declaration.

It can be implemented but I'm skeptical that it's correct. You might try convincing Python-dev.

I don't particularly need this functionality. It was just something that seemed counter intuitive to me.
I discovered this while working on a python to javascript compiler. I'll probably implement the compiler to allow overriding with __name__ as it seems more intuitive to me that way.
Hopefully cpython will be changed to work that way too.

This is not a bug report, as Python works as documented. 
Double underscore names are defined as *reserved* for the interpreter, with the ones actually in use having defined meanings.
type.__new__ sets several internally used attributes on new classes. The attribute look-up mechanism for classes looks at them first before looking in __dict__, which is for attributes of both the class and its instances. Here is another example similar to yours.
>>> class C: __dict__ = 1
>>> C.__dict__
dict_proxy({'__dict__': 1, '__module__': '__main__', '__weakref__': <attribute '__weakref__' of 'C' objects>, '__doc__': None})
>>> C().__dict__
1
__dict__ is not writable, but __class__ is. You can already rename a class if you really want:
>>> C.__name__ = 'bizarre'
>>> C.__name__
'bizarre'
Conceptually, this seems the right way as one normally would not want the name of the class to be the default name for every instance.
>>> C().__name__
Traceback (most recent call last):
 File "<pyshell#12>", line 1, in <module>
 C().__name__
AttributeError: 'bizarre' object has no attribute '__name__'
If you really want instances to have that also, then also do as you did.
There are other class-only, not for instances, attributes:
__mro__ and __subclasses__ and perhaps others.