Omega has raised some very good points.
I don't know if you noticed that when Neo was trapped in Mobil Avenue he wasn't wearing his usual Vatican priest garments but was dressed identically to what Mero was wearing in Reloaded.
As to what happen to Neo at the end of Revolutions well my guess is that it has something to do with what Smith kept saying to Neo at the end of Reloaded, " You haven't figured it out yet, still using all the muscles except the one that matters, I want what you want i want everything."
When Neo reached Machine City, he told the head machine (or Godhead) that the program Smith had become too powerful and would overrun the city just like he had done in the Matrix.
Now if you compare the end scene with the crucification, it is Christ just before he dies on the cross who says "It is finished", in Revolutions it is the head machine, i therefore think that Neo not only is in every person connected to the matrix but is also in the head machine and it was he who said "it is done" just like the Oracle said "everything that has a beginning has an end, Neo" through Smith. Remember that Smith always called Neo, "Mr Anderson".