Lex would be a good enemy for the two of them. He is of course Superman's nemesis, but he also rivals Batman in intelligence, wealth and technology. However, if they fight against two villains, I think Joker would be a bad idea. Great villain and all, but instead of having two masterminds, the one working with Lex should be more of a physical threat, someone who can trade fists with Superman. The hero duo is composed of Batman, who is a tactical genius, and Superman, who is able to move the moon with his bare hands. The villain team should be composed similarly. A tactical genius and a strongman.
Metallo maybe? They'll probably introduce kryptonite in the movie, so Metallo could symbolize an embodiment of that, and he too is an interesting adversary for Batman (since he is sort of a freak of technology, which is much more in Batman's field than Superman's).
Also, regarding Flash, I've been thinking a lot on a good villain for the movie. I hear a lot of people demanding Gorilla Grodd, and as cool as Grodd is, I think that would be a bad idea. Why? Because this movie is going to be Flash's origin story. With that come a lot of necessary steps.
1. Introduce Flash before he becomes the Flash (Wally West or Barry Allen? I like both so I would settle for either one).
2. Introduce his friends, family and most likely the love interest as well before he becomes Flash.
3. Set the premise for the transformation (the lightning doesn't come out of nowhere, it's part of a lab accident. Before the accident occurs, there needs to be an explanation of what the lab was actually doing).
4. Transformation.
5. Discovering his abilities.
6. Costume. When Flash superspeeds, he vibrates through solid objects (kind of like Shadowcat in X-Men) and that means clothing as well. He wears his costume because he can't vibrate through it, and therefore, he doesn't have to save the world naked.
7. There also has to be an explanation for why he uses his powers to become a super hero. Not everyone would just do that, and go risk their lives to save people simply because they have the power to do so. There has to be motivation for his heroism.
Then he can become the Flash. Now I can finally get to why Grodd doesn't fit with Flash's origin story. Because introducing Grodd takes a long time as well. Here are Grodd's steps:
1. Establish Gorilla City before they learn of humans and before humans learn of this alternate evolutionary path. Preferably, Grodd is also established in this environment, so you see how he is before he learns of humanity.
2. Humans and Gorillas learn that the other exists (and no, I'm not talking about the gorillas we all know are real. These are gorillas that have evolved our intelligence, but still have the appearance of our ancestors, or similar ones anyway). There has to be visible human reaction to the gorillas as well as gorilla reaction to the humans.
3. Grodd's opinion of humanity has to be clear as well. He views them as an error in evolution.
4. Whatever technology he will be using also has to be established. He finds a crashed alien ship and salvages advanced technology from it. Sometimes he has devolvers that convert humans to apes (although the fact that he supposedly calls these devolvers is ridiculous based on his established ideology), sometimes he has a mind control device. I don't care what he has, but he will have to have something if he is to fight a hero faster than light.
5. Grodd acts out against humanity. Whether Flash comes and stops him or this time or if he gets to complete one crime so Flash knows what Grodd will be trying to accomplish in those other ones is optional.
Of course, these steps aren't written in stone, but it should give people a clear vision of how long it will take to establish those characters. And here I can finally get to my point: Introducing Grodd at the same time you introduce Flash will take too long. The movie won't even properly start until an hour or so has passed OR they skim through it, in which case the characters won't be properly established, which can easily ruin the movie.
This does not mean an origin story has to start with a lame villain. Quite the contrary. Many successful origin stories are successful and have good villains. But if we look closely at them, we see that the villains are usually highly connected to the hero, and therefore, they can be established alongside the hero, sharing scenes with the hero, saving valuable time and getting the audience to the good stuff they were waiting for much sooner.
In Batman Begins, the main villain was Ra's Al Ghul, whose character was established while Bruce Wayne's character was established, during his training. Scarecrow was then introduced as Ra's Al Ghul's right hand.
In Spider-Man, Green Goblin (or Norman Osbourne should I say) had a lot of scenes with Peter Parker. Why? To minimize the scenes away from the hero without limiting the necessary introduction this important character needs.
Same with Amazing Spider-Man. The scenes Curt Connors was established in usually involved Peter Parker.
The only exception I can think of to this is Lex Luthor in the original Superman movie. They didn't even meet until the end, but he still manages to be properly introduced.
Anyway, I think Zoom would be an ideal villain for a Flash origin movie. Grodd could be a very good villain for a sequel, where Flash's character has already been established and we can view Grodd's origin story in between Flash fighting crime (or maybe a minor villain before the big fish...or big ape...shows up).
What do you people think? Zoom? Grodd? Some other villain maybe?