The villain should be Amazo in combination with Lex or, as I prefer, Savage.
There isn´t really a story I can think of that enlightens every important aspect needed that satisfyies me as much as Amazo-Savage does. Some important aspects are: charachter development, team dynamic and a original/proper JL villain. Amazoo is perfect for that because he can help show that "the whole of the sum is greater than the parts" and what I mean by that is that he´ll be absorbing powers defeating each hero at first, forcing them to work together. He´ll also help us see that one mind is efficient, perhaps much more efficient than the JL as newbies but it can never exceed that of a synchrnoized JL lead by Superman. What´s also great is that you get the mystery of some bigger fish as well as great origin stories. I mean Savage has a cool background and portraying Amazo as a confused anti-hero as in JLU would be cool.
CSA isn´t that good because you loose the contrast between the charachters . I don´t like the idea of comparing 2 charachters that are both new. I also dislike any alien invasion because it has been done to much nor do I like space villains like Doomy or Brainy because I think they belong in the MoS movies. I´d rather have some original JL villain and hopefully it will be someone that makes sense. I need to read the Starro comic because a lot of folks hope that´s what´s gonna happen.
So: Amazo-Savage for sure but Despero, Grodd or some interesting sourcerer could work but come on, we all know we want white martians (MMH) for second movie, the CSA for the third and DS for the fourth. That´s how you do it. You also make damn sure he´s been teased via Orion/new Gods + old Gods/Wonder woman in her movies and that DS was the one who sent Doomsday to Earth for MoS 3.