I was think of a theory about the Dragons' location for a while then it led me to think back to Rave Master with the Dragonrace with Let, Julia and Jegan where they came from called Makai.
What if the Dragons went to a place similar Makai, a different world, that would explain why Dragon's would be rarely seen or why Natsu's, Wendy's and Gajeel's dragons disappear so inexplicably and when Acnologia appears and vanishes when it attacks.
And with a world full of humans, I don't think anyone could miss a dragon sighting or if a farmer's live stock was raided by a dragon.
I also believe that E.N.D will not appear until the very end of the Tartarus arc, where he trashes Fairy Tail and leaves to destroy the Dragons.
What are your thoughts.