Well, it's not a huge plot twist, but I think most of us were expecting Gray to be off training on his own, or hunting down leads on Zeref; however, it's entirely possible he's doing just that, considering his father was doing the same thing with END.
I guess the interesting thing we have to ask is who is the biggest threat, END, Zeref or Acnologia. Acnologia did seem to be making an active effort to kill Marde and destroy END's book; whether that was just a matter of prudence or genuine fear is up for speculation. And Zeref fully expects END to destroy him, but again, whether he's going to battle END or just means END is the only one with enough power to actually hurt him is the question. Right now, my money is on END being the strongest character in the manga.
Outside of Acnologia, the strongest dragon we've seen has been Igneel, and he was battling with only a fraction of his actual power. Chances are good that he's on par with Acnologia. And he was said to be unable to beat END, and Atlas Flame implied that END is the greatest threat he knew of. I personally can't wait to see it all go down.