The book Jus Divinum cogently lays out the case for Presbyterianism versus other models for church organization, such as Independency and Prelacy. Here is a link of an extract from the book comparing Presbyterianism and Independency :
Having been a member in the past of various Independent Reformed (Baptist) churches, I think Jus Divinum rather accurately reflects what I observed in the Independent churches. I found that Independent church officers tended more than Presbyterian church officers to make subjective judgments lacking objective evidence, which would have come under more scrutiny if Independents had to report to higher church courts. But, of course, Independents lack higher church courts, so there can be a tendency to get away with decisions based upon unsatisfactory evidence. There can be an over-estimation by Independent church officers of their power to discern inward grace in prospective communicants, and a lack of sufficient carefulness in addressing observed sins of word and deed. A lack of accountability can tend to this result, in my opinion.
The Manual of Practice of the Free Presbyterian Church of Scotland ( see http://www.puritans.net/news/fpcs062804.htm ) is more sound, and it is consistent with the principles laid out in Jus Divinum. In chapter one the Manual emphasizes the need for the session to base decisions of who can participate in communion upon objective observable evidence, yet it commends the session to exhort the individual to probe his own heart, which only God and he can do. The individual is not left to imagine that the church’s permission to participate in communion may equate with divine permission. So the possibility of inappropriate assurance of salvation for the hypocrite can be reduced.