Actually, I just watched an interview snippet of Orlando in which he says that Will gets "dark," but not "Darth Vader dark." (Eek! Even Orlando is making Star Wars comparisons. :p) To me, this means Will probably won't become "the new Jones" - unless that "office" does change drasticlly.

I'm suddenly leaning towards Davy Jones getting some other kind of closure, probably death, probably at Jack's hands. I say that because Bill Nighy said in an interview that his Davy doesn't get married at the end of #3. I don't know what else would "neutralize" Davy Jones (since I'm guessing his end is necessary for The Age of Piracy to end).