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My personal opinion is to include all public APIs. Names that are omitted from __all__ may not come up in pydoc, and it is surprising when I use "import * " in the interactive interpreter to play with a module and there is something missing.
To mitigate the risk of breaking code, I have been maintaining a list of the modules affected at <https://docs.python.org/3.6/whatsnew/3.6.html#changes-in-the-python-api>, which warns that extra symbols will be imported in 3.6.
On the other hand, there are other cases where people wanted to exclude APIs from __all__; I pointed out two at <https://bugs.python.org/issue26632#msg266117>.