I imagine they will have different storylines. They will be the same "types" of races, but they might even have slightly different names? Who knows. But I doubt the stories will be exactly the same, because you cannot tie into the world of Eorzea with the world of Vana Diel, however I expect to see some similarities and some things that will make FFXI players grin a bit.
Like people have said, one of the beauties of FFXI games is the fact that they will reuse old designs in new games, with newer fresher stories and development.
Long Live Vana Diel.