For those unfamiliar with American Presbyterianism, the Presbyterian Church split as most bodies did during the Civil War (1861-65) and even after Appomattox, the bodies remained divided.
These Churches both operated under the revised Westminster Confession (1646) which had been modified after the American Revolution to remove the notion of an Established Church and a magistrate that could call for Church councils to meet. This was incompatible with the American Experiment, and consequently they changed the Confession to reflect not only the new reality but a sentiment many shared. Some Presbyterians continue to reject this modification and want an official established Church.
The Northern Church fell under the influence of theological liberalism during the latter part of the 19th century. Beginning in the 1700's largely in Germany this movement was heavily engaged in textual criticism and a re-casting of the entire Christian faith. The introduction of Darwin's ideas only helped to accelerate a large scale deconstruction of the Bible which continues today. Its danger was that it retained historical doctrinal terms but redefined them to mean something else. The average person in the pew often didn't realize what was happening.
By the dawn of the 20th century the Northern Church like many other Protestant bodies was compromised of people who questioned Scripture and almost every doctrine basic to the Bible, while others sitting beside them still were clinging to forms of historic Christianity.
This was the time of the Fundamentalist reaction. The Fundamentalists were so named because of a series of books put out at the time that tried to identify the doctrines key to the Christian faith, the non-negotiables as it were. Some Presbyterians started to embrace this thinking as well as the rising tide of Dispensationalism with its modified Pre-millennialism.
In the late 1920's, J. Gresham Machen left Princeton's theologically liberal climate and taking some of the faculty with him he formed Westminster Theological Seminary in Philadelphia. In 1936 the conservative remnant of the Northern Presbyterian Church again led by Machen formed the Orthodox Presbyterian Church or OPC.
In the South, theological conservatism held on for another generation and it wasn't until 1973 that a large group left the old Southern Church, known as the PCUS and formed the Presbyterian Church in America or PCA. There's some debate about the reasons behind the formation of the Northern and Southern remnant denominations. The OPC was definitely driven by theological concerns and later split with the Bible Presbyterians who had largely embraced Fundamentalism and the Premillennialism and legalism that went with it at the time.
The PCA it has been argued was formed more out of the backlash to the 1960's counter-culture, the shift in government and the Supreme Court rulings. The Church was divided on where to stand or not to stand. The PCA being rooted more in this social narrative rather than a strict theological construct, ended up being more of a big-tent or umbrella movement. It brought many into the denomination that were not as concerned with maintaining the old Presbyterianism of previous generations. Some of the issues related to this continue to vex the PCA to this day...how strictly to adhere to the old forms of Presbyterianism.
The mainline Northern and Southern Churches continued to drift into apostasy and eventually rejoined and formed today's PCUSA....Presbyterian Church in the United States of America.
Just don't confuse the PCA with the PCUSA. They are quite different. One is adhering to a form of Bible-based historic Christianity, the other has embraced modernism and more or less rejected the authority of the Bible.
Creating a Middle-Tier
As a Congregationalist I whole-heartedly reject the entire Presbyterian model, but for various reasons I continue to find myself having to interact with it. There are some core reasons and many practical ones. I'm going to address some of the here and attempt to explain this in a way that won't be too difficult to understand.
I believe the Church has a universal aspect...the Church in all nations across the world and all the individuals within it. And I believe this Church is manifested locally in Congregations.
As Christians we're part of the universal Church which itself can be discussed from several angles and in different senses, and like Paul in Acts 13 we assemble locally.
Despite Presbyterian and other denominational arguments, nowhere does the Bible present to us another level, another organizational tier between the local and universal aspects of the Church which is what a denomination is. The one argument they have is Acts 15, the Council of Jerusalem.
It is important for local Churches to not live in isolation. Their elders, and yes there must be a plurality of Elders, not a single Pastor which is novel to the New Testament...should reach out and meet with other leaders of congregations. Presbyterianism seeks to institutionalize this relationship creating a middle-tier and consequently they generate a massive host of ecclesiastical forms to go with it. This is what happens with Denominationalism. You're trying to bind local Congregations together and create a body between the local assembly and the Universal Church.
Supposedly this brings about unity but in reality it erects forms which the Scriptures know nothing of and these forms (like Confessions, Books of Church Order, Committees, Regional Presbyteries and the like) actually prevent local congregations and Christians from participating in the full life of the Universal Church. Rather than leave openings to bridge difference and yes the danger of error, it erects walls. Walls which protect, but which also divide.
Does Acts 15 support this? I don't think so. This was a meeting of Apostles over a doctrinal issue. Their declaration claims to be inspired by the Holy Spirit...'it seemed good to the Holy Ghost and us'...
No ecclesiastical body can claim that today and if they do, they're far out of bounds. The Church does possess authority granted by God but this authority is only within the bounds of Scripture, it's not Apostolic in nature. The Apostles under inspirational guidance could give pronouncements like that. The Church today does not possess that type or quality of authority.
It could also be argued James presided over the meeting which if anything would grant a more Episcopal flavour to the assembly.
Looking for Unity with a man-made form
Again, Churches need to be in contact with each other. Different congregations can meet and discuss issues affecting their area. They can meet and discuss the status of persons which have been excommunicated.
Presbyterianism and other denominations are trying to create bureaucratic structures which hold the Church together and prevent people from bouncing around between congregations and ignoring discipline and accountability.
True Unity is found in the Biblical Forms and the Holy Spirit
I would argue the Holy Spirit binds the Church together. Man-made forms do not help in this regard and frankly men do not have the authority to erect them. And, they don't work anyway. You can end up with denominations where the leaders are bound to forms (Creeds, forms of discipline) but the congregation itself may be largely ignorant. No one will come out and say it to me, but on more than one occasion I've received the impression they like somewhat ignorant people...they're more compliant. The essence of spirituality lies more in the direction of compliance with the elders than learning the doctrine of Scripture, learning to think...and hence learning to question.
Presbyterianism is largely content with this because they believe the essence of the Church, its real core lies with the mid-level body, the denomination itself. It's really about the Presbytery as they call it, or the regional body. The various Presbyteries meet in a General Assembly, usually once a year.
Plurality of elders does not mean plurality of offices
The Bible uses the word Presbytery in 1 Timothy 4, but there's no reason to believe this council of elders was anything more than the local church body...a local group of elders or Bishops as the terms seemed to be used interchangeably in the New Testament. The Overseer or Bishop the Episcopos is the same as the Elder or Presbuteros. I'm not going to dive into that here, but I think anyone who looks at the issue will find this is the case. Deacons are the other office, but their position is one of service, not authority. Many Baptist Churches mistakenly call the Bishop/Elder the 'pastor' and the Deacons are really what the Bible calls 'elders'.
But what you don't find in Scripture is an office called 'the pastor'.
Some Presbyterians try and get around this by claiming there are two types of Elders...Ruling and Teaching elders. They base this on what I believe to be a questionable reading of two passages...Romans 12 and 1 Timothy 5.17. The Teaching Elder they call the Pastor and though in the PCA, they claim the Ruling and Teaching Elders essentially hold the same office, their practice indicates otherwise. The OPC goes ahead and just creates two distinct offices, the Teaching and Ruling Elder.