Only shooter games released recently you can do the main story in co-op would be Halo 3/ODST and Borderlands. There's also LFD 2 which isn't the traditional story mode but you can play co-op through each campaign.
MW 2 has the co-op spec ops mode, which is similar to what SC will offer. Army of Two 40th Day has a co-op campaign but I don't know if I'd pay full price for that game.