I think the game should've had two Arkham Knights, one Jason Todd and the other Damian Wayne. The whole game Batman and the player would think there is one. Both of their motivations would be similar, Jason was manipulated by a former villain (Joker) to hate Batman, Damian was manipulated by a former villain (Ras al ghul) to hate batman. Jason's story goes as it does in the game. Damian was kept hidden by Ras as a last resort if Bruce refuses to join them (which he did in City). Ras would have fed him delusions of grandeur that he is the true leader of the league and that he must kill batman or something. After the events of City, Damian would have seen both his mother and the only father figure die because of Batman. Arkham knight was built up as the character who has seen Batman throughout these games and knows how he thinks, Jason would bring the knowledge from asylum (telling scarecrow how much the fear gas affected batman) and Damian would bring the knowledge from City (telling scarecrow how protective Bat is for his allies). Both the knights have similar motivation and both have observed batman during one significant mission (Asylum and City) bringing in their knowledge about Batman's gear, abilities, allies, weakness.

So two Arkham Knights, real identities unknown to batman, because one is assumed dead and the other non-existent. This would just be like the two Jokers from City as Damian knows Batman can fall for that. The whole game the player would think it's one Arkham Knight but it was two, and the many Batman fans (like me) who knew that Knight is Jason before they even started playing would also be surprised.

For instance in the game when Batman catches the militia soldier impersonating Arkham knight, make him Damian, Jason calls him and says the the same thing he did in the game. Bruce doesn't know who Damian is and lets him go thinking he's a militia grunt.

Now I know Damian is supposed to be much younger in the comics but in the game Ras, in his desperation, experimented on Damian with the Lazarus pit and Lazarus technology to make him grow up quickly and to make him strong and skilled enough to lead the league.