Whether denominations are a problem depends upon your vision of the Church. I don't see any evidence of a single international hierarchy in Acts. I see churches in different locations that were loosely in communication and communion with each other, but that at times differed on things significantly. People like Paul and Barnabas visited them, mediated, brought the Gospel to places that didn't have it, and renewed it in places that they thought had strayed. I understand that you can ignore the untidiness and treat this as if Peter was the Pope and there was something like the Catholic Church, but I think that's significantly misreading the evidence.
So the question is: how was our unity in Christ supposed to be reflected organizationally? I don't see any problem with individual congregations that cooperate as much as possible, and maintain fraternal relationships with each other. I'm a member of a fairly connectional denomination (the PCUSA). I think that polity makes sense. But I certainly wouldn't want to see every church in the US part of the PCUSA. I would like to see all of the churches accept each other as fellow parts of the Body.
I view the 16th Cent as God's judgement on the Western Church, rather like the tower of Babel. The Church had come to confuse itself with the Body of Christ, and not surprisingly, this arrogance had led to significant abuses. Fracturing the Church, much like fracturing the languages, was intended by God as a protective measure to make a reoccurrence less likely.