You might check the heater hose routing. The hose coming from the intake manifold (supply) goes to the lower connection on the heater core while the hose that connects to the upper heater core connection provides the coolant return back to the water pump. This helps to purge the air from the heater core and in turn, provide for more heated water to go through the core. If the hoses are hooked up in reverse, an air pocket remains in the heater core without easy access out.
As Steve mentions, checking the amount of flow going to the heater core is also a great suggestion.