These two things are different, but unfortunately Commissioner system, a purely administrative mechanism, is mixed with Local Government System, a local bodies' basic amenities system.
As far as your query is concerned, i think you are asking about the difference between Commissioner System and the Local Government System 2001. Dear! Local Government System of 2001 was more than an ordinary local bodies system. Through this system, control of civic amenities as well as the general administration of district was handed over to a politically appointed, indirectly elected, Zilla Nazim. Professional administrative hierarchy of Commissioners, Deputy Commissioners and Magistrates was abolished and almost all the powers were divided between Zilla Nazim and Sessions Judge of the District. So,in short, the difference between them is that in Commissioner System, career civil servants run administration while in Local Government system Nazims are vested with the authority to control the reins of services and general administration.
Yes, as you can see, this Local Bodies System of 2001 had several shortcomings. It not only politicized the administration but also divided the local politics on ethnic and political ground. Though this system ramped up the quantifiable betterment in basic service delivery (in a few districts), it severely undermined the general public administration and law and order situation. Commissioner System is the need of the day and now it is revived in Sindh for the betterment of general administration, though law and order is still in the purview of police and judiciary. In all the other provinces, a hybrid system is in vogue.
The best way is to introduce a local government system that contains both the elements of Commissioner System as well as Nazims/Mayors'. Although Local Government System of 1979 can provide better solution, yet MQM and her local politics is the biggest hurdle in reaching any trade off between the two systems.

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still searching for my soul..............