I’m wondering if there is a way to replace an object with an object in another scene, while assigning all the materials of the old object to the new one and parenting all the children of the old object to the new one–basically the new object takes on all the settings of the old. Of course, I would have to assign the materials to the faces. Can this be done?
There are a couple of ways to approach this. The most flexible way is to start thinking in groups and then have your master object deploy the group into the scene via dupligrouping. You can parent to the Empty of course, but the group itself acts kind of like a loose collection of related objects. To replace an object in the group just add the new one to the group and remove the old one from the group.
Another way is to swap the actual datablock of a like typed object. This means you can swap a mesh for mesh, but not a curve for a mesh. The problems you will faces with datablock swapping are that of materials. By default, materials are applied to the datablock and not the object but that can be changed. From the start, set the material on your master object to Object mode then build up the material. When you want to swap the mesh out, just import the new object and link the new object datablock to the master object datablock. After you have linked in the new datablock you can discard the imported or source object. For multi-material meshes you will need to consider material index between the swapping meshes as well.