There was always a kind of strange disparity between the history and those dragon slayers' claim their dragon masters disappeared so short time ago. As far as we knew, the black dragon, Acnologia, was the one and only dragon still hanging around. Otherwise humans were living in peace everywhere, which doesn't seem possible if dragons were still common. The weakness in the writing is the fact nobody ever said to Natsu & Co that dragons haven't been around for a long time, so there's no way they could have been living with dragons just a while ago. Even if it's possible it could have happened in some remote area if the dragons never really flew around to be seen by anybody, but normally people would still deny it.

Nevertheless, I feel like Mashima did manage to wrap his lore quite decently. It's actually a fine detail how everything should have gone according to the plan, save for the fact Zeref couldn't hold his head together for 400 years simply waiting and waiting. I also like the fact that killing Zeref will kill Natsu as well. That'll give Fairy Tail something to think about, as if things weren't complicated enough otherwise! Maybe they will just seal Zeref inside another crystal right next to Mavis.