User blog comment:Miskos3/Fairy Tail Chapter 486: The Fourth Guest, Review/@comment-4507125-20160524082154/@comment-7418318-20160524085419

Maybe he hates what he has become.

I think the Dragons didn't know that using Dragon Slaying Magic would eventualyl turn their pupils into Hybrids.

So basically Acnologia signed up to learn a new magic to fight in the war, but instead his body was changed into something no longer Human. Something people might well consider monstrous. Going by the impulsive behaviour that many Dragon Slayers show, it's also likely that the process put strain on their minds, changing how they acted and thought, weakening their self-restraint.

It isn't hard to imagine that Acnologia might have accidentally killed innocents either as collateral damage, or due to losing control of himself.

Add all that together and it's no surprise he might come to despise the being that turned him into this monster. And to make matters worse he didn't just have to endure this torture for a single Human lifespan, but is cursed with eternal life and thus endless suffering.

So his behaviour might be part taking revenge on the Dragons too far and part making sure that a being like him will never again come into existence.

Though that would only explain his hunting of Dragons and Dragon Slayers, but not why in F-Rogue's timeline he would slaughter most of mankind. Maybe F-Rogue was so good at hiding that Acno's frustration over being unable to find the very last remnant of the Dragons got the better of him and he started to just indiscriminately blow everything up to drive Rogue out of hiding or demolish his hiding place and the 90% of mankind were just collateral damage.