At first this is quite a good idea, as a stepping stone to a Justice League movie
Have the heroes join up over the course of several movies instead of just one (Especially since the Justice League does not have something like S.H.I.E.L.D. to gather them systematically) with the two big ones getting their own movie
Also the first thing that comes to mind is the animated Worlds Finest (The 97 Dini one)who is quite a good take on how and why the two heroes would react to each other
Then I hear them quoting Millers batwank of a comic and my enthusiasm slips a bit
Then I hear that they let Nolan produce I can no longer muster anything other than a resounding "MEH"
At least the will be finding a new Batman to replace Bale
But how to threaten the man of steel? Well let's see
1)There have been no hits of Kryptonite yet (But that does not mean that it can't be introduced)
2) Since Nolan is involved we can probably rule out magic
3) Red sunlight is still a factor, and have been made into a weapon in both the comic and the animated universe
4) Match him in strength (There's plenty to choose from even non-kryptonian)
5) Other ways to bypass his invulnerability (Personally I remember; sonic, electric, light and neural based weapons used on him to great effect)
None of these even have to be individuals, the green lantern movie already hinted at project Cadmus, who have the most advanced weaponry in the world (And without seeing the movie, I am guessing that after the man of steel movie they probably have some Kryptonian ones too)
Or Intergang the hightech terrorists with alien weapons, which could also hint at the sequel where they need the whole Justice league.
Both are probably too big for this movie but the idea is the same, as long as the mooks can hurt him their numbers and the fact that they are extendible make more than enough tension for you to not need anyone as powerful as Superman.
(Could "just" be Luthor arming some mooks with hitech weapons capable of hurting superman, maybe Metallo , who even without his Kryptonite heart is more than capable of trading blows with supes, for the big finale)