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Currently Popen.communicate accept str is universal_newlines==True and bytes if universal_newlines==False.
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.

> What to do if stdin doesn't have `encoding` attribute? Convert to bytes using filesystemencoding?
If choosing an encoding, it probably makes sense to default to the same as for when universal_newlines=True, namely locale.getpreferredencoding(False).
> Adding `encode` parameter for .communicate doesn't looks elegant.
Also see issue 6135 (to allow setting encoding).

Uhum.. Universal Newlines is being deprecated.

No it isn't. There's some issue about a 'U' parameter somewhere that is being deprecated, but that has nothing to do with this issue.

See also issue16903.

See also Issue 27273, proposing to use text string input as an indicator to turn on universal_newlines=True in the higher-level functions. I’m not excited by either proposal, but I find the other one a bit more palatable.
IMO allowing text string input to communicate(), but returning byte string outputs would be a bad idea. It would have been better to call the universal_newlines=... flag "text_mode".