The Gospel Coalition has two concise articles making the case for both Presbyterian and Congregational church government. Presbyterian polity is defended by Mark Jones, and Congregational polity is defended by Hunter Powell. Both are interesting reads.
Why You Should Be a Presbyterian
by Mark Jones
Despite what you may think, Presbyterian ecclesiology is not primarily defined by churches governed by elders, but by churches governed by presbyteries. Presbyteries can encompass the elders of a local church, a regional church, and what is termed a "general assembly." This view is established from the oneness of the visible church. Based on the sufficiency of Scripture, Presbyterians hold that the church is governed jure divino (by divine right). There are certain fixed principles in the government of the church. We hold that Christ has blessed the church with the Scriptures, church officers, and sacraments. In doing so, Christ has "ordained therein his system of doctrine, government, discipline, and worship, all of which are either expressly set down in Scripture, or by good and necessary inference may be deduced therefrom" (Presbyterian Church in America Book of Church Order).
Why You Should Be a Congregationalist
by Hunter Powell
Fear, Loathing, and Extreme Democracy
Congregationalists, Presbyterians, and the reformers have all historically agreed Matthew 16:18-19 and Matthew 18:15-18 deal with excommunication and church discipline (see, for example, the
Catechism questions 83-85). These
verses, therefore, define where church power is located. To cast members out of
communion with the visible church is the most awesome and fearful task given to
the church in Scripture. If, as the Reformation taught us, the definition of
the church is the Word and the sacraments rightly administered, then locating
the power to remove a person from the sacrament of communion will delimit the
boundaries of church government. Heidelberg