That could work as well. Though to be honest, in my own opinion of course, I think this set up would/could work as well for future films involving Superman:
1. MOS 2: Use Lex and the Elite. Now I know some say that the Elite wouldn't work within the DC world that MOS first established, but given on how the filmmakers would probably want to go off of the consequences from Superman having taken Zod's life, along with him trying to further establish himself to humanity as its protector and hero, I think the Elite would really work well here.
If anyone's seen the animated short, "Superman vs the Elite", it really executes the whole concept of Superman having to deal with the idea of killing off his villains and how the Elite tries to antagonize him into doing so, wholeheartedly believing that it's the way that any real hero should do, etc.
Plus, given that we're building to a world where Superman will come across the other DC heroes at some point, I think the presence of the Elite could give the idea to Superman that being a part of a group of real heroes who share similar ethics like him would help Earth better, thus setting him up to start looking for those heroes in the JL film.
2. MOS 3: It could deal with Brainiac, though I think taking Superman to space to attack him would work better here, just like how they did for the animated film Superman: Unbound. The reason why I say that is because it could get rid of the issue of why Superman didn't call for aid when Brainiac arrived, thus allowing Superman to be pushed to his limits from Brainiac, and it could further introduce more DC worlds and end with the conclusion that Superman will be the bridge for humans and aliens all around the galaxy to unite, thus possibly ending with a epilogue scene in the 31st century where we see the Legion of Superheroes, a group of alien heroes that were inspired by Superman's heroics.