It seems as though the popular opinion through posts on this site suggest that Batman and Superman will team up to beat up some baddy at the end of BvS:DoJ. Rumors from Braniac to Doomsday, and even Luthor having a hand in the latter's creation understandably spark people's attention. However, they are not necessary in this film, because this film is not 'The World's Finest", it is Batman vs Superman. Another point of worry I have noticed is the fact that too many heroes will appear in one film, an issue I intend to answer for as well.
Zach Snyder said in an interview on the creative process behind the upcoming film that in discussions for what to do next with the Man of Steel (having just had him fight another of his own race, and a battle trained one at that) they posed the question of who could they face him up against next. The answer was Batman, because who else to face after a God, but a Man? This tells us specifically, the conflict of the film will be between Batman and Superman. We don't need any other bad guys, and if we do, it should be the suggested Victor Zsasz that Batman is tracking down at the start of the film (just so we can see a detective Batman). But no other big bad guy is necessary because you have BATMAN AND SUPERMAN on screen fighting! This even lends itself to the DKR comic, as the climactic fight is between the two titans themselves. In fact, if they tried to shoe horn in another villain, it would feel too much for the movie and it would be Spiderman 3 all over again.
Now some may say, "well the whole film can't be them fighting! it's just gonna be a bunch of action and boring then!" to which I say, think not back to MoS (Which I'll grant got boring in fight scenes) but back to Watchmen. Say what you will about the end, but Snyder's ability to incorporate the political implications of a world with Superheroes in it was perfect, and if you have read the DKR comic, you'll know that Miller himself delves into the politics of it just as much. In this way, the start of the movie will likely deal with the political/philosophical implications of living in a world with a Superman, and whether or not people feel safe, or if he should pay for crimes, etc. Superman will likely stand trial in Washington, meanwhile Luthor and Wayne are competing for contracts to rebuild. A deal will be worked out that Superman will work for the government and be asked to take down the dark vigilante Batman, a plot constructed by Luthor himself. This will take us to the fight. So most of the movie won't even be a Superhero movie, but instead, more of a political intellectual thriller that happens to have Superheroes in it.
Now as for the rumor of Batman breaking into Lexcorp and seeing that Luthor has secured Zod's body, I love this idea, because it is a perfect easter egg to set up the next film. We should see Lex starting to collect things, but not revealing himself as a villain yet. Even his contracting cancer from coming into contact with Kryptonite and having to shave his head should be in this film. This could be done as an after credit scene with him in the doctors office being told, and then having treatment started.
To deal with the question of multiple Superheroes, think of the world logically. If there were a multitude of super powerful beings on Earth, would each stay in hiding until his/her respective film? No, of course Batman would have to figure out if this Alien that fought in metropolis can be trusted, of course Aquaman would express his anger over the giant distorting beam that attacked his ocean. If he waited until Justice League, we would be confused why he took so long. Of course Wonder Woman would be sent to do reconnaissance on this super powerful man that could threaten her people. In fact, this is an issue I had with Marvel in some of their films, that things seemed so disengaged. Bringing multiple heroes in is a necessity in this film, because it shows us the world of which we are apart. Also, we should not worry too much about them stealing screen time, as I suspect Wonder Woman might have fifteen minutes, and Aquaman one monologue, and any others, less than a minute (i.e. Cyborg being built/a 'Flash' of red going by).
I have been thinking of writing a more succinct article on the exact plot (in my mind) of the film. Let me know in the comments below if you would like to see this. Also please leave any comments you have on what I have wrote here, whether you agree, disagree, or are interested by it at least.