2. Flags _soft_ downvote people unlock easiers
3. Mods have a ""super"" flag which is the ranking equivalent of aging a post pre-maturely. So the weighting algorithm calculates the post as being much older then it actually is allowing it to slide off the front page faster.
There's no reason why a few people clicking 'flag' should ruin the experience for everyone else.
It's true that the effect of flags isn't perfect in every way, but we have to evaluate this on a whole-system level. I'm not aware of any way to make the whole system work significantly better (otherwise we'd have done it already) and certainly getting rid of flags wouldn't be one.
There's no reason to have a 'flag' link once a story hits the main page, for example.
Anything is preferable, at this point, to the methods used. Perfectly good articles are getting dropped and it comes across as censorship.
Is the secret handshake that important to the success of HN? Why throw newbies for a loop or make them have to think about this?