I think everything is the same... even the cutscenes. I remember someone commenting that it was in fact really weird to fight Syndrome with Syndrome.
Syndrome is really popular though, so I think a lot of people played through the Incredibles playset using him... like I don't really see Syndrome hanging on store pegs anymore. Not the same case with Davy Jones though... I see him everywhere... probably not too many people out there who defeated Davy Jones using Davy Jones.