This is my idea that I came up with yesterday after the Superman/Batman movie was announced and could fit into the movie universe created by Man of Steel. Not only does my idea introduce Bruce Wayne/Batman but also Lex Luthor,Barry Allen/Flash,Braniaca and Kryptonite!
In the sequel which could take place soon after or even years after the events of Man of Steel, Bruce Wayne would travel to Metropolis as himself and at a news conference (which is being covered by Clark Kent) announce a partnership alongside Lex Luthor between Wayne Enterprises and LexCorp in an effort to rebuild Metropolis after the alien attack by Zod. Lex would proclaim that he would also go after Superman who is also responsible for the damage and has managed to stay out of the limelight other than saving people here and there.
Of course Lex Luthor has an agenda and other than go after Superman he plans to harness Kryptonite which is now a part of the earth after Zods "world engine" added elements from Krypton into the earth's atmosphere and thus Kryptonite was created. Lex has his own personal laboratory secretly testing on the newly found element and one of his lead scientist is...Barry Allen!
Bruce is not only in Metropolis for his partnership announcement he is also interested in learning more about Superman and due to his superior techonology is aware of Lex Luthor’s secret plans to harness the Kryptonite. Bruce (dressed as Batman) goes to investigate some of the left over wreckage from Superman and Zods encounter and discovers pieces of Kryptonite for himself. This also leads to Superman and Batman interacting for the first time and actually coming to blows. The fight is even due to the Kryptonite Batman is holding and the Kryptonite in the surrounding area.
Later on, After Batman and Superman realize what Luthors plan is they also find out that Lex has harnessed some of the left over alien technology from Zod and has begun making a version of his classic suit which is infused with Kryptonite(unknown to Superman who does not know he is allergic to the Kryptonite yet). The use of the alien technology also leaves open a potential for Braniac in a future movie(he could be behind giving Lex the information on how to make a suit to kill Superman).
In the final fight scene Batman and Superman are rushing to find Lex at his secret laboratory where his suit is when there is an explosion at the laboratory(cut to a shot of Barry Allen working there). Out of the rubble Lex Luthor has finished his suit and the final fight takes place.
In a post credit scene when Superman and Batman are talking Superman's super hearing kicks in and he hears something tells Batman to get ready for another fight and when a blur finally appears then settles the camera pans up and reveals the Flash in all his glory setting up his appearance in a solo movie or in the Justice League film.
Just to clarify the explosion at the lab in which Barry would get his powers would not be due to kryptonite(ala smallville powers) but due to his own experimentation there. This could be explained by Barry in a future movie.
This is just my idea after learning of the movie yesterday. Let me know what you guys think.