Mainly the bureaucratic nature of it. Preserving HN's minimalism has been a priority because it's the kind of thing that's so easily lost; like a frog boiling itself.
Yea, I get the hesitance to invest in this. Nobody is going to select/admit reasons like "Because flagging is a mega-downvote and I don't like this story getting attention," even if it's the real reason. We don't know how accurate or actionable Slashdot's drop-down choice moderation was, either. Even if people are honest about their intentions, what is actionable? Not much I guess.
If it's overhead for the flagger, they could be presented with a single multi choice question, eg:
What most deserves flagging: a)item title b) item content c) hn discussion d) something else
With different users presented with different questions to build up a picture.
Flags could be recorded even if the question isn't answered, but with you reserving the right to weight ones without answers less.