I just finished Arkham Knight and it was a great story. I highly recommend it. It rivals many movies.
The main villain in the story is The Scarecrow, with a new comer named The Arkham Knight as a main antagonist.
There's also appearances by Two-Face, Penguin, Poison Ivy, Man-Bat, Deathstroke, Harley Quinn, Firefly, Pyg (who I personally hate with an undying passion) Deacon Blackfire...and The Riddler.
Now if you've played the Arkham games you know the Riddler is just...there. But is he really?
Think about this for a second.
In the first Arkham game, The Riddler BREAKS into an Asylum JUST to mess with Batman. As you're playing as Batman your mind is on the main mission of catching the Joker, but you always have this little gnat just fluttering in around the corners of your eyes. A gnat you continue to swat away, but never really get rid of. Once you beat the joker...is the game finished? Nope...you have to catch The Riddler.
Same thing goes for Arkham City and Arkham Knight. Which brings me to my point...who's the true main villain of the Arkham games? I think it is The Riddler.
For most people he's the last person you catch. Even after the stories main villain and antagonist. This makes sense with the very character of Edward Nigma, The Riddler. He's an egomaniac to the ninth degree. He makes Batman prove himself worthy to even see him, let alone fight him. He lets Batman deal with villains he feels are lesser villains than himself and being that he's an egomaniac he MUST be the main event.
The Riddler is the last villain you battle. So to me, The Riddler is the true villain of the Arkham Series