1. You are basing the majority of your consternation on your own personal experience, no? Assuming
that this is the case, let me respond from my own personal experience.
I have seen most all of the "Presbyterian" governed churches, both continental and reformed (Dutch) fall into heresy and some even into apostasy over the past 30+ years. Think back also even back in the 1800s when Charles Finney came onto the scene when many Presbyterian churches followed his methodology and some even his damnable heresy. Not much of a motivation for someone to get involved in a Presbyterian run denomination, eh?
2. Over the past 30+ years, the judicial based system of Presbyterianism has failed to discipline even a handful of their clergy for clearly teaching heresy, e.g., John Kinnaird, an elder in the OPC (Orthodox Presbyterian Church); see e.g., here: Orthodox Presbyterian Church Endorses Teaching of John O. Kinnaird
. Other fundamental errors the OPC has committed have been the adoption of John Frame's "Multi-Perspectivalism" (I was a student of John Frame when at WTS Philly), where biblical "truth" can vary depending upon the "perspective" of the reader. Another major error was the OPC's promotion of what is called "The Hermeneutic of Trust". What is THAT? Well, whatever the General Assembly, under the rule and guidance of its 'officials' rule is to be embraced by all. In this case, the OPC GA ruled that various contradictory views of creation are all compatible because they do not contradict the "Standards"; WCF, WLC and WSC. Sooooo, an elder may (permission granted) to teach Theistic Evolution, Framework Theory, 6-Day/24hr literal creation, et al and they are teaching 'truth'.
3. In my own personal studies on this subject, I have never found a convincing argument for a Presbyterian form of government. I see Acts 15 as a one-time instance in the infant Church and should not be taken as a paradigm doctrine for church government. I won't go into detail in enumerating the various alleged 'proofs' for that form of government, most of which are based upon very weak exegesis and presuppositions.
4. Historically, true Congregationalism was extremely close in doctrine to the Presbyterian/Reformed churches. All one need do to see this is incontrovertibly true is compare the Westminster Confession of Faith
with the The Savoy Declaration of Faith and Order
. Congregationalists believed in a plurality of elders and a deaconate. They did differ, however in that they did not erroneously divide the eldership into two; Teaching Elder and Ruling Elder, making ruling elders a second class of men.
5. True Reformed Congregationalists often have a fellowship among them whereby they share many of the same interests and assist other churches among them when needed, e.g., the ordination of men to the ministry and disciplinary matters.
6. Lastly, there is NO PERFECT CHURCH because they consist of fallen members and office bearers. You will find errors, in every form of church government, and injustices in discipline. What I find most odious is that there is a noticeable similarity between secular governments and the Presbyterian/Reformed governments where a select group of elevated men determine not only policy, but also doctrine and life of all. If those men are in error, the entire denomination is negatively effected. To be fair, this can also be said of independent churches where the "Pastor" can become the 'dictator' and bring the entire congregation into ruin. My confidence rests in God who has ordained all things, including the formation of false churches, false teachers, and false professions of faith among members who preach and teach a false gospel. The Wheat will grow among the Tares until the coming of our Lord Jesus Christ. But the true people of God will by the Spirit be given wisdom to discern these things and be preserved from falling away.