One of the points that Simons/Burns have been trying to make is that all beaureacratic organizations function in similar ways. Whether it is the police department, a newspaper, a drug ring, a school etc. The power structures are similar and the limitations placed on those who are "on the street" are similar. In all five seasons there are back-to-back scenes in episodes that are almost exactly the same except that it's a different organization.
I would disagree that Gus and Freeman are pretty similar - Gus is a very by the book kind of guy. Freeman created an illegal wire tap.
I agree about Scott - but you have to remember that Simons/Burns have also said that they reject storytelling that is moralistic. Think of it as a Greco-Roman mythological story. The point of the story is to show how much power these institutions (gods) have. In the end people get zapped with lightning because they challenged the institution. I wouldn't be surprised if Gus gets fired and Scott rides off into the sunset - because the paper has too much invested in this whole homeless "series".