I think in comparing the modern vs early church we need to be careful not to make some errors in looking at the church merely as a form or a fashion, a way of doing things. The church was never a physical structure but rather a spiritual building.
I do see some definite shortcomings of the American style of "doing church". To me, the pastor down, CEO structure is fraught with problems. It creates an atmosphere where those who are "under" are often vying for position and trying to climb the ladder so that they too can be "spiritual". It is not always a matter of a heart that desires evil things but is often a function of the concept that the really spiritual people are in church leadership positions and we all want to be spiritual. I also see that it fosters a clergy / laity mentality which I believe is not borne out in the NT. I see shortcomings in the board run democratic system as well in which the pastor is a hireling and is under the scrutiny of the board.
Having said that I have also seen some problems with the modern day house church movement. I have seen those who simply don't want to submit themselves to anyone else so they do their own thing.
I am not an early church historian but I have noticed a few things about the early church. It was a people transformed by God, born again, and filled with the Holy Spirit. It was a people who were passionate about their savior. I notice that the church was seen as a universal body of believers and the local expression was the church in a particular geographic area and not the particular group who has rallied around a doctrinal nuance. I see eldership in each city or region. These men were chosen for the same qualities that we find mentioned in Paul's teachings. Their positions were not heirarchical as in a corporation but they did have charge to watch over the flock and to lead the church in the things of God. I see that because of the spiritual qualities in these men that they were worthy to be followed as they followed Christ. So, there was a submission by the body to this God-ordained leadership. In similar fashion each member of the body was submitted to one another in love. They were all in each others' business so to speak as they lived life together and had close and intimate relationship in the Lord. This is what mutual submission looks like. I notice that the church met in peoples' homes most likely because of the atmosphere of persecution and/or the cost of building a structure. It did not seem important to build a building or an organization. People desired to win the lost and build Christ in them. I notice that there were apostles, prophets, pastors, teachers, and evangelists that were given as grace gifts to the body to minister to the body with the end of producing maturity so that the body, fully equipped, could more effectively minister the gospel to the world. These men were sometimes vocational and traveled, but more often than not were resident in the local body functioning as they lived life with the body. The body understood that every joint was necessary to supply its part as it was empowered and energized by the Holy Spirit.
As time went along it seems that the Jews followed the pattern of the synagogue in their churches. Buildings were build and meetings were held in those buildings. I don't think the building is the problem but rather the heart of the people who build it. I don't think home meetings are necessarily more Biblical than meeting in a building but it is the heart of the church that conforms to the Biblical standard or falls short of it.
The thing we must consider is where we are at in relationship to where God would have us be personally. As a teacher in the body I long to see a time when the church in my area would be willing to see the grace gifts given to equip the church operating city wide rather than being confined to one building because "we don't quite see that issue like you do." I would like to see us able to prayerfully come to the Word together to settle doctrinal differences. I would also like to see us be OK with ongoing discussions of things like pre-trib or post-trib as things we don't have to settle today but can still be in intimate fellowship regardless. I am not talking about an ecumenical movement but rather a unity and fellowship of the body of true believers in a city. Obvious heresy and error must be called out and dealt with. But that is what the giftings of apostle, prophet, evangelist, pastor, teacher and the city wide eldership is called to do. That is part of overseeing and equipping.
I am always blessed when I look at the church in areas like North Korea, North Vietnam, Cambodia, China, etc. These people do not divide themselves like we do and their focus is, to me, closer to the focus of the NT church. But then again, we could be in that situation before too many years.