I've done the tour, from Eastern Orthodox to Charismatic, Mennonite to Pentecostal, Non-denominational to Salvation Army and have had some time to consider these matters. In fact, that is why I chose the path of study that I did. I wanted to find out what the churches were doing wrong so that I could do it right.
Problem 1: Church replaces Ekklesia
In my studies, I discovered the origin of the word 'church.' It comes from the Greek ekklesia, which means 'a calling out.' Remember reading about John the Baptizer in the NT? He was baptizing people in need of repentance. Do you remember where John did this? Was it in Jerusalem? NO. It was outside the city in the Jordan River.
Ekklesias were first exercised by the Greeks when they found that their city state govts. were becoming too corrupt or oppressive. The citizens would publicly call for an ekklesia (assembly). If enough people came out and refused to accept the govt.'s authority, the government would collapse.
When Jesus preached in Jerusalem, he eventually was rejected and was called out to preach in areas near the Sea of Galilee. People would come out of their towns to greet him and worship him.
What do the churches of today do? What is their ekklesia, their calling out? For Baptists, they usually do an 'altar call' at the end of the service, asking if Jesus has called them out of their sinful lives to walk with the Lord in obedience. If someone comes forward, the pastor and/or elders and deacons will pray with these people and will decide if they are ready for baptism.
While John baptized for repentance, people were baptized in the name of God the Father, the Son, and the Holy Spirit. The submerging represents the death of the old person and the emergence of the new creation, governed by the Holy Spirit.
After that happens, (s)he goes back to church the next week and does the same thing (s)he did before the baptism. Do you see the problem?
Church has taken the place of ekklesia. People do not leave the comforts of their community, families, and friends to be baptized. The 'calling out' is more of a 'welcoming in,' meaning that instead of non-conformists making up the assembly, we now have conformists making up the assembly, joining the community, families, and friends. This means that along with the Holy Spirit calling out someone, we also have the peer pressure of the church calling people into it. This leads to people joining the assembly for different reasons; some are baptized into the assembly of God, while others are baptized into the church community, not having the spiritual experience of being "born again."
Eventually what happens in Baptist churches is that the born again believers recognize that leaders and several of the congregation are not guided by the Holy Spirit and obey the call of the Holy Spirit to the real ekklesia (calling out), leaving the church to fight over matters of doctrine, their music, the colour of the carpet--worldly concerns.
Though different denominational churches have different methods of initiation and indoctrination, the results are the same. The church in the city or town with the 4 walls is doomed to become too oppressive (legalistic) and/or corrupt because a genuine ekklesia hasn't taken place. We see this happening today with clergy and deacons who become too oppressive or too permissive. These extremes result in either neurotic congregations of mules trying to gallop like horses (read: Baptists) or the inclusion of abominations like common-law marriage, idolatry , homosexuality, alcoholism, etc. (United).
Most fights between and within different denominations happen because of theology (vs. sound doctrine/teaching). Do you know who the first recorded theologian in the Bible was? It was the serpent! "Did God really say...?" Theology means the word/matter/things of God. So like the serpent, one theologian challenges the authority of one's statement, creating conflict and strife instead of the harmony that emerges when people humble themselves and submit to God. The process of true debate, dialectic inquiry, demands confrontation in order to arrive at a higher "truth," which is assaulted by various critics until another "truth" emerges, creating an endless cycle of confrontation.
Some churches, which I won't name, are a mixed bag of strictness and permissiveness, who either ignore the sin and strife or try to hide it behind closed doors. The image of unity is shattered only when a sex scandal is reported in the media, and even then, the church will try to resolve the matter as quickly and as privately as possible by monetary compensation and/or the transfer of the offending party to another church.
Problem 2: Emotionalism replaces worship
While true worship is responding to God's glory and includes praise, a response to God's attributes, the churches create their own kind of "Praise and Worship." While the more traditional churches (the ones packed with Seniors) feature older hymns with Scriptural references, the "big box" and non-denominational churches engage in emotionalism to reach a spiritual high, much like the pagans used to do. Sexual elements are common, as are loud bands with various musical instruments and sermonettes to direct the "Praise and Worship." Some critics of this practice suggest that it even invites demons to join in their worship. You can read this for yourselves.
http://www.piney.com/Charismatic.html
The Temple of Christ
Acts 2 pretty much describes the ekklesia (assembly) as it should be. No walls, no membership lists; the new temple of God is a fluid collection of individuals who come together for events and projects like a movie crew. When the project is over, people go their separate ways and reassemble as the Holy Spirit orchestrates. My name for this form of impromptu worship and action is "Ad hoc fellowship."
I pray for the people in the churches, but I don't worry about the churches or how people perceive Christianity because of the public debates and the church splits that occur . As these churches become more corrupt and oppressive, more ekklesias will happen and more people will join the body of Christ.