Had you told me before San Diego Comic Con International last week that Warner Bros. would announce a movie starring Batman and Superman together on the big screen in live action, I'd have been incredibly excited.
Of course, some of that enthusiasm has been tempered as the film's presentation came in the form of a dramatic reading from The Dark Knight Returns and David S. Goyer told fans that the film would be called Superman vs. Batman or Batman vs. Superman. Frankly, I have serious concerns about the filmmakers' ability to take the tired old tropes of the meet-fight-team-up syndrome and translate them to the screen in a way that doesn't reduce the characters to the lowest common denominators of superhero fiction.
Don't get me wrong; I loved Man of Steel and will be the first guy in line for tickets to this film when it comes in two years. Still, I'm not without reservations. For instance...
It's going to be hard, making a Superman sequel, to create a film in which Batman shows up, throws a bunch, and doesn't seem like the bad guy.
In fact, we've had problems with this kind of thing before, but comics readers, I daresay, are a bit more forgiving provided you resolve it all within one issue or arc. Batman seemed pretty confrontational with Superman when he appeared in Byrne's The Man of Steel, for instance (likely a major contributing influence to this film even if--like last time--it won't be acknowledged since the Byrne era is considered unfashionable at present).
A similarly chilly relationship forms at the start of Batman/Superman #1 by Greg Pak; it seems that, in the modern era, the way to go about establishing Superman and Batman as a team is to be sure everyone knows they "earned" their friendship.
Of course, nobody seriously believes that's not just what will happen in a prospective Batman vs. Superman movie. Still, you don't want to introduce a character who's basically a villain and then have to spend time redeeming them. You'll want to make sure at the outset that the readers are on board with both of the heroes, even if you have to spend some screen time you didn't want to on developing motivations early.
Bear in mind, too, that Superman's final battle in Metropolis has evoked such a visceral response in fandom--and it's an issue that the filmmakers have said they'll address--that even though he's the hero of the first film and is carrying over to the sequel, it still may not be surprising to see Superman treated as the antagonist early. Batman may get a spotlight in the first act, in which case expect a fair amount of grumbling from the usual quarters about how DC can't make a successful movie without him (which is of course silly).
I'd just as soon never see Kryptonite on the big screen again. it's been done so poorly, so consistently, culminating with the absolute silliness of Superman Returns, that honestly we could take a nice, long break from green K and I'd be alright with it.
Sadly, the presence of Batman almost guarantees that they'll tackle the Kryptonite ring that Superman gives him "in case of emergency," or at least did so in the post-Crisis era and will likely do again in Batman/Superman in the New 52 once this first arc is resolved.
The problem that Kryptonite poses is that it could potentially wipe out all of the good Man of Steel did in terms of establishing Superman's power scale. Two devices that are badly overused to bring Superman down to the level of mortal men are Kryptonite and some kind of removal of the sun. If he's got a prolonged battle with Batman, even if it's only in the first bit of the film, expect at least one--if not both--of those elements to come into play.
Making them seem stupid
We can assume that it's more likely than not Superman and Batman will be manipulated into fighting, or manipulated into a misunderstanding that causes them to fight, by the film's "real" villains.
That's a slippery slope; you don't want to make the characters look too stupid or easily manipulated, but the meet-fight-team-up thing is only really effective if the fight carries some weight so it also can't be figured out and resolved instantaneously. The best way to handle it would be to establish the villain first as a master manipulator. Perhaps Luthor or Brainiac could fill the role?
In Man of Steel, we got more Clark Kent, and a different take, than ever before. Same to Lois, for the most part, and to his parents to an extent.
With much of his supporting cast coming back, we assume that they'll be sure to give Clark a little time...but making it a team-up (or fight) movie means giving Batman time, as well, and that's going to eat into "unnecessary" things like developing the supporting cast. It's how they've been doing it in the comics for about fifteen years now; the supporting cast in the Superman books barely gets a couple of pages in any given issue, while the superhero stuff gets more and more interconnected and impenetrable.
Here's hoping that, in the desperate pursuit of the Justice League movie, they don't break the Superman franchise they just finally fixed.
There's no need to tell his origin again. Or if there is, you can just do it subtly and in dialogue. Have him tell Superman, briefly, "Something terrible happened in my past. I lost people close to me, and I never want that to happen to anyone again." We've already seen Batman's origin on the big screen more times than anyone ever asked for, and the "daddy issues" that the two share is not a compelling enough reason to do it again.