Just call me Batman because I have done a little detective work. Here we go. According to actress Molly Quinn (via Worlds Finest), next summer's animated release from DC will be based on the Superman: Brainiac by Geoff Johns featured in Action Comics #866-870. Molly knows this because she will be the voice of Supergirl. This reminded me of a survey Warner's released in 2010 regarding possible upcoming movies including one based on the same story:
Superman: The Lost City of Krypton
Superman learns of an evil robotic artificial intelligence called Brainiac, who travels the universe, miniaturizing whole alien cities, including their citizens, which he keeps in bottles for study. When Brainiac threatens Earth, Superman has no choice but to hunt him down, only to discover that among the bottled cities in the robot's possession is Kandor from his homeworld of Krypton. Somehow the Man of Steel has to figure out how to defeat this superpowerful A.I., while protecting this last vestige of Kryptonian society. From Geoff Johns' popular comic series. Rated PG-13
Putting 2 and 2 together, I am predicting the movie will in fact be called The Lost City of Krypton and that this synopsis is spot on. Also, based on previous releases, expect to see it in June 2013 as an excellent tie in to Man of Steel. The title also skirts association to the worst animated DC movie ever made, Superman: Brainiac Attacks which was released at the same time as Superman Returns. In the case of the animated movie and the live action films, lets hope that the second time is the charm.