The context of some scenes is unknown at this point. The way Superman was kneeling to Lex, and the way Lex positioned his hand on his head in "almost" care was the first scene I really thought it could have been a possibility towards the clone theory. There are other possibilities to the scene, but it was hard for me to not consider how this came across.
It just strikes me as almost the Star Wars sith like control, where he kneels to the master so to speak awaiting command.
Obviously it could have a totally different context and that's not a clone as well. I stand by the idea that it's worth speculation though for fun.