It would be really nice to be able to modify the ResID, SegID, Chain Number, Atom Name, etc when you save in PDB format. Mainly for creating ligands for further computational studies; docking, MD, and so on.
It could be done with a preview style window. With drop down menus to select the segment or residue number you want to rename (in an adjacent text field or something). There could also be a list of chains and segments that could be dragged to reorder; for example ABC-->BAC.