2to3 can convert doctests, it just can't convert the *output* portion of doctests. because they are arbitrary strings and not syntactically valid Python code.  Since turning on this flag would require recognizing something in the output portion of the doctest (which 2to3 doesn't handle), it can't be turned on by 2to3.

On the other hand, it seems like it wouldn't be too hard to write a special purpose script to handle this specific case...since I don't know 2to3, I don't know how hard it would be to integrate such a special purpose script.  (I do remember Benjamin saying 2to3 really ought to have a plugin system...so my guess is the answer is "not too easy").

In any case, as Nick said, that would be a separate RFE, and will likely get nowhere without someone volunteering to write the script/patch.