Control Theory has developed over several decades its own set of more or less formal modelling techniques that are suited to the automatic control of dynamic behaviour of complicated manufacturing systems and processes. The Internet Society is addressing new Enterprise-Control Integration challenges for agile Business to Manufacturing purposes which enlarge the traditional setting of Automation Engineering to the Systems engineering approach. In order to cope with the increasing complexity of integrating Intelligence/Information-intensive manufacturing automation within the networked Manufacturing Enterprise, Automation Engineering should be integrated in the Systems Engineering approach for achieving a holistic approach that treats in fine the operational manufacturing system emerging from an ad hoc combination of formal and informal partial models. This paper emphasises, that a Holonic Manufacturing Execution System Engineering approach should be the quintessence of such an approach along with other relevant scientific, industrial and educational areas dealing with information and Intelligence control and management issues in agile manufacturing.