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Well, I wouldn't call this "severely flawed", but I can say
we've been running into problem number 2 quite a few times.
We've got quite a few 'mutt' users and the standard
formatting for subject lines of forwarded emails is 
[<author>: <oldsubject>]. We've also got a support tracker
running, but people send their support requests to the
strangest places, so we end up forwarding emails to the
support tracker quite a bit. All mutt-users have now changed
their 'forward_format' variable, but it's still irritating:
try forwarding an email you got from a mailinglist (for
example: [staff]).

That said, I'm not sure I would turn on a configuration
turning off all subject matching, command parsing, etc.
Those are pretty useful features, after all. I'd rather find
a less intrusive way of specifying
classes/identifying/setting attributes, though I haven't got
a proposal as to what that less intrusive way should be.