Yes, it seems the seeds of the various reformation movements were germinating right from the start with the central issue being where the seat of authority resteed....Could one enter into relationship directly with God, or could the great unwashed only access the divine by subjecting themselves to the authority of a bishop and the clergy. It was a Roman structure that won out in the end...even the Pontif, borrowed from the old Roman Pagan Pontificate
While you are right about the dispute between Rome and the rest of the churches, you have mis-timed it. The ideas of the reformation were alien to the church fathers who simply took Jesus at his word and participated in the church he founded. By the way. Bishops are described in the New Testament, right down to their qualifications.