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I like to accept both str and bytes if universal_newlines is False and raise explicit exception for bytes if universal_newlines is True.
Looks like universal_newlines for bytes doesn't make sense, also we prefer to use str everywhere. Bytes should be used if it is really byte-stream or if unicode cannot be passed by some limitations of underlying OS etc.
There are couple dark corners:
1. What to do if stdin doesn't have `encoding` attribute? Convert to bytes using filesystemencoding? Raise explicit exception? Adding `encode` parameter for .communicate doesn't looks elegant.
2. How .communicate works on Windows? I see completely different implementation of this method for win32.
I need some time to investigate before publish proposal to python-dev list.