Not infrequently I tweak placement of pins on a symbol to make my schematic wiring cleaner.
However sometimes I have two copies of a symbol that I would like to have differing pin layout… is it or will it ever be possible to edit these independently, similar to how you can tweak footprint instances in pcbnew?
New schematic format in V6 is planned to have symbols embedded in the schematic, similar to how footprints are embedded in board file. Most likely it will be possible to do in place edits that will only affect that particular instance of the symbol on the schematic.
Until the updates in V6, it is probably best to make a project library to hold the variations that you need for each project. Granted, that might mean reinventing the wheel each time you need to make the same change. At that point (if it is a common variation) it might be worth it to save the modifications into a personal global library (or libraries).