This could get into a really nasty argument with no redeeming features. So let me say first that in my opinion there are valuable features in each of the three main systems.
That said, it's been the tradition of the majority of Christians since the beginning that the church is organized around the bishop, in the apostolic succession. This predates the monarchical system where the bishop is separated from the people by a layer of clergy, but ties to the older system where he is the chief pastor of the major church of the major city of the area, and all the other churches of the area are "daughter churches" founded by and from the bishop's church and acknowledging him as their religious leader under Christ. Through him and his powers of ordination and confirmation, the clergy and laity are tied in the apostolic succession directly back to those called by Christ. The church as a whole is led, either by a bishop specially called to a leadership role (e.g., the Pope), or by a collegial/conciliar unity among the bishops
The fault with episcopacy as a system, and the more hierarchical versions of it such as Catholicism, is that the human opinions and attitudes of the bishop will shape the behavior and policy of those under him spiritually -- and not every bishop will be the humble servant of the Holy Spirit that he ought to be.
Presbyterianism preserves the virtues of collegiality but at the cost of having a firm leader -- the old proverb that "a camel is a horse designed by a committee" amply defines the problems presbyterian polity faces. Nonetheless the idea of authority vested in the clergy and exercised collegially preserves at least a modicum of apostolic faith in the midst of temptation.
Congregationalism preserves the historic autonomy of the local church, but at the cost of any reasonable system of making the spiritual unity of the church real also on a mundane, secular plane as well. And in practice it often turns into the local congregation being led down the primrose path by the clergyman whom they call and who is answerable only to his own local lay board -- who may be handpicked by him. The net result is at best a skewing of the apostolic faith towards the particular elements of it that are of particular interest or motivation in the mind of that clergyman.
A system that preserves some local autonomy, some collegiality among the clergy, and the authority of the bishop within the bounds of defined doctrine changeable only by full church council, seems to me best.
