The Council was an inovation, an extension of the regional synods that had long been a feature of Church government and one that gave a powerful layman a leading role in the Church. Justinian, who fancified himself as a theological equal to any bishop, sought disaterously to settle the Monophysite dispute. In the 8th Century, Leo the Isaurian and his successors, caused turmoil in the Church, including the use of a "council" to impose iconoclasm on the Church . It was to avoid this sort of imperial meddling or "caesaropapism" that led the Church of Rome to develop papal government. The struggle between the medieval pope and the western emperors cannot be properly understood except in the light of the history of the Byzantine state Church.
Yes, but Justinian was obliged by the Council he called to prove his own Orthodoxy, thereby showing that in matters ecclesiatical, councils called by the Emperor for the peace of the Church are superior to the Emperor. His confession of faith is now a hymn in the Divine Liturgy said immediately after the second antiphon.
It is nice to hear that you regard papal government as a development. But a universal council was hardly an innovation: besides the local councils there is as precedent the Apostolic Council recorded in the Acts of the Apostles. It was not a local council of the Church of Jerusalem, although the local bishop, St. James, the Brother of the Lord, presided, but a council to decide matters for the entire Church.