So, I have been re reading Scott Snyder's run on Batman recently and I had an epiphany while reading the Court of Owls story. I really think that they will be the main villains of the film and that Riddler will be a red herring who is supplanted by them. Namely, I think Riddler is killing people connected to the Court and they will eventually reveal themselves in the third act.
I know this theory is not original at all, but I think it's really valid for a few reasons.
1) For one, having a murder mystery where we all know who the culprit is over a year before the movie releases would be a misfire IMO. Yes, we still get to see Batman work it out (and seeing the detective angle get more focus is a major bonus), but I think there must be some third act twist.
2) In the Fan Dome event, Matt Reeves mentioned that this film will be about Bruce realizing that the corruption in Gotham goes way deeper than he realizes and the mystery will force him to explore the city's history (and the history of the Wayne family). This is exactly what the Court of Owls arc in Snyder's run is all about. At the beginning of the story, Bruce mentions how he feels the city is always watching over him, and that he sees himself as restoring it to it's pure, uncorrupted state. But the revelation of the court of owls makes him realize that the City isn't necessarily pure at all and that the wealthy have been conspiring to keep the poor down and to control the city since it began. He also learns that his great grandfather was forced to build bases for the Court before he was killed by them.
Again, this story literally hits on the exact themes that Matt Reeves is talking about and I think it fits.
3) We know Reeves is somewhat influenced by Scott Snyder's run. He's mentioned Zero Year as one of the big influences on the film (Riddler's motivation is similar to that story, a young and brash Batman in a more makeshift suit, slight hints that Bruce and Alfred will clash in the film, etc). Therefore, if he's read Zero Year, he's clearly looking at that whole era of Batman really heavily (rightfully so, as Batman IMO was the only DC character who prospered in the New 52, with all of his main titles firing on all cylinders for at least 2 years).
4) This is more minor, but the card that Riddler leaves Batman does have an Owl on it. Yes, it could be a complete coincidence, but I think it lends some Creedence to the theory (I also know I'm not the first to note this, but I wanted to bring it up).
Basically, when I read Court of Owls last weekend I was having an epiphany that the story basically touches on all of the themes that Reeves teased for the film.
I really hope this is true. Riddler will be an awesome antagonist (and I really hope he's left alive and in Arkham at the end) but we've seen Batman take on crazed killers on film before. The Court of Owls would add such a big dose of nightmare fuel to the movie, and I think it would give the film a real identity.