The Justice League movie would connect Batman to a larger universe filled with heroes like Superman and The Flash. A lot of people would like to see a Mr. Freeze done right in a new Batman franchise. I'd like to see Mr. Freeze on screen again after Schwarzenegger's "cheesy" performance in Batman & Robin, but the chances are slim for him to appear on screen because of this certain character..
Captain Cold! Captain Cold is one of Flash's greatest villains so it is very possible he'll appear in a Flash movie. The odds that DC will have two different ice-themed villains to star in their movies is very unlikely. Batman has a large rouge gallery and there are still many bat villains that haven't been adapted to the big screen (Hugo Strange, Killer Croc, Hush). Flash's rouges can be to complicated to adapt to the big screen (Gorilla Grodd, Mirror Master) or just to simple to be the main villain of a movie (Trickster, Captain Boomerang). This leaves a hand full of villains who could be the main match against the Flash (Reverse-Flash, Captain Cold, Heat Wave?)
It's still possible that Mr. Freeze could star in a new Batman movie, or that Captain Cold won't be used at all! This is my opinion on why Mr. Freeze won't be in a new Batman franchise. Comment your thoughts below!