This is a great thread, if only because it lets me point out that most of this stuff is fixed in Perl 6. :-)
It's going to take me a while, but I think it would be valuable if I responded to most of these. First, the OP...
The behavior of -M, -A, and -C is intentionally differentiated from the bare values returned by stat(), so that's probably not going to change.
The mkdir problem will be solved by making the mode an optional named parameter that goes before the list of directories if you do specify it.
And finally, print FH @list is illegal several ways in Perl 6. First, there are no bareword filehandles in Perl 6--they're just regular variables. Second, indirect objects are no longer differentiated by the absence of a comma, but by the insertion of a colon. (The reason it doesn't work with comma in Perl 5 is that print wouldn't know whether it's supposed to treat its first arg as an object to print to or a value to be printed to STDOUT.)
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