I am starting to understand whats going on now. Rouge was lying the whole time and is the evil one! Originally they opened the gate and all 10,000 dragons came through but Lucy survived in other to come back and alter time. However Rouge (Who was turned evil somehow) discovered that she went back so he went back too to stop her. Now, Rouge has killed the first Lucy but she succeeded in helping second Lucy realizing what was wrong so there is a chance the future will be changed after all.
It also seems that all 12 keys are needed to close the gate so Yukino will have to get her butt outside to the gate soon
I agree. I have a theory that all the dragon slayers weren't from the present and originally came from 400 years ago. The dragons didn't actually vanish, the dragons slayers did due to time travel or something. Also, Natsu being from 400 years ago would explain why Zeref would know him. (And another thing I will point out, is that on Natsu's Fairy Tail membership card, it says "Age Unknown". And during arc with Laxus he couldn't leave the barrier made for 80 year olds soooooo... It's just a theory though...