No, Jolly Roger is not Davy Jones. look at their past, they are different. Jolly Roger became skeletelly due to being cursed by Amo Dorsi, the voodoo witchdoctor and Davy Jones became squiddy due to Calypso's betrayel(She started it and that's that!) besides i highly doubt they could have Davy Jones being Jolly Roger or Jolly Roger being Davy Jones even if they wanted to.
As for my vote? I vote partnership.. highly unlikely though, but for me? one can always dream.. My two favoritest Pirates characters working together.