While the Joker and Lex Luthor are both villains, they don't play the same roles. Would you say Commissioner Gordon can't be in all of the Batman movies because Dan Turpin isn't in all of the Superman movies? Of course not, because different characters have different roles. Lex Luthor is a prominent recurring character in the Superman mythos, whereas the Joker pops up from time to time to cause havoc. Lex Luthor practically owns Metropolis and as such there is no reason he can't be in every movie.
They do somehwat play the same roles. Ask anyone, not just comic book fans who batman's arch enemy is and they'll say Joker. That's just public perception. You ask them who's superman's arch enemy.. they'll say lex luthor. They are both the antithesis of their corresponding heroes whether they pop up from time to time or not. But Nolan was able to bring in a villain that is relatively unknown to the public and he still made it work. The same can be done with Superman. Lex is not needed. I think at this point the audience would rather see someone new introduced that they havent seen before. It would be new and exciting.
You can't put Turpin on the same level as Gordon. Gordon, in everyone's mind, is important to batman's war on crime. That's just common knowledge. Turpin, on the other hand, is not vital to superman's stories. He's a relatively unknown character. I hadnt even heard of him until the animated series. He doesn't have that reputation of being superman's connection to the police.
Yes LEx is a prominent recurring character but he doesnt have to be in everything. IF so he'd be in every superman story no matter what and he isnt just like joker isnt in every batman story.
We've seen lex in every superman movie already and look at some of the backlash that resulted in it with superman returns. There was a lot of negative sentiment... ppl thinking "another lex story?" Lex can take a break. Everyone knows he's there. Even if they omit him in the movie you can place things in the movie that suggest he's there. Billboards, buildings, newspaper headlines..
Emperor Palpatine in star wars is important to the mythos of star wars but they didnt show him until the second movie and even then it was glimpses. They didnt fully show h im until the last movie. And he was the manipulator or the saga.