Perhaps promoted content should be labelled as such, eg an orange 1px border around the listing. If adding a new story in to the mix that could have a green 1px border to highlight it was out of normal flow too.
To the extent we're able to be objective, we try to be. YC founders and companies get their titles edited and suffer the same penalties as everyone else. The only advantage YC founders and companies might have is the ability to recognize each other from the orange names.