The nice thing about this series is how it creates SO much potential for restarting/reviving interesting in some characters' origins. Tampering with history and their minds leads room to wonder who, if anyone, might have originally been a villain (If you read the Flash, there was this guy, the Top). Were there members of the JLA who were criminals, rounded up, and brainwashed? Could the Justice League have really been just as bad as the Crime Syndicate, but with a bunch of people brainwashed (ala Squadron Supreme). Brad opened the door for this.
I doubt DC would be so bold, but that would be a nice thing. Suspicion as to who was really good/bad, etc. Was the Flash merely another Johnny Quick or something? Doubtful. I am just having fun pondering. I mean, if a writer chooses to mess around with the Atom, then you can mess around with a lot of other characters. Maybe Arthur hated humans and was going to go to war with them. I like this.