So we found out that E.N.D is Zeref's brother. With that innocent little Natsu picture, it was easy to forget that E.N.D is actually the creator of Tartarus and the most terrifying demon that Zeref has created. It possibly scares Acnologia. I read some comments about people wondering if the current Natsu had all of the memories, as few as they were, of when he was Zeref's younger brother. I do not believe this is the case.
I believe that E.N.D did create the dark guild Tartarus. He was at some point everything E.N.D is said to be. Terrifying, evil, and powerful. But at some point, the Dragon King festival battle happened. It was a battle between humans, dragons, and demons. Perhaps the guild was created in preperation for that, who knows. But during this battle, Igneel did in fact fight E.N.D. He was no match for this demon. In his last ditch attempt to save himself from the demon, he used his dragon memory manipulation magic on him in order to cause E.N.D to not kill him. Maybe make him think he actually did when he didn't, or something else. But due to the funky ass nature of dragon magic, it affected this resurrected corpse in a strange way. It reverted him back to his original form. Baby Natsu. Seeing this little kid and wondering WTF just happened, he took this kid away in order to protect him.
Then stuff happens and we have current Natsu. I like the idea that he was put into a coma along with the other DS's and they were programmed to wake up in the year 777.
Another theory I'm fond of is the Gajeel being related to Acnologia one. Also some people are saying that Acno might have trained Natsu. People say that isn't possible because he would have smelled the same as his dragon form. I don't know what to think of this one, but I don't think that if they did meet, that Acnologia spent any real amount of time with him. He very well could have passed by and put whatever is on Natsu's right arm, on him while he was asleep. The arm Acnologia was missing is the same arm that Natsu now has bandages on. Perhaps there is a correlation.