See, I'm fairly certain the big plot twist of the movie is going to end up being that Lex has been manipulating Batman into fighting Superman all along... because Lex knows Batman's the only person in the world who could probably defeat Superman. Being that they're basically the two big corporate moguls of the DCU, there's no doubt in my mind that Lex and Bruce are familiar with each other. No matter how evil he may be, you have to admit that Lex's defining trait (aside from the fact that he absolutely despises Superman's very existence) is that he's a fucking genius. There isn't a doubt in my mind that Lex is able to figure out that Bruce Wayne is Batman. Especially a Batman that's been around for 20 years. I'm sure that's why Batman has Kryptonite in his armor, because Lex made sure he'd have it.