Oh, to rephrase my other statements, I change "How it should go" to "what I would like to see from the DCCU".
Anyway, let's begin;
1) MAN OF STEEL 2
Now, personally I think the villain should be the one many big Superman fans want to see; Brainaic. Well, as his origin is a little inconsistent, I never really minded the one they gave him in the Animated Series, but that or the one about him being from Colu.
Story can be simple, but great if executed right. Brainiac sends drones to Earth, Superman defeats them, discovers Braiancs plan to assimilate Earth or shrink one of it's cities and destroy. Confronts Brainiac, and the rest is Earth struggling, physical and psychological battles between Superman and Brainac.
Hell, they could introduce Kara if they want. How to do Brainiac? They have a lot of choice. Personally, I would like to see his personality and overall presence have the feel of that of the animated series. And have Corey voice him too, as that voice is perfect for Brainac. The psychological battle could be the fact that Brainiac hold the history and knowledge of Krypton (as he either destroys Krypton or is an AI like in the animated series).
They could have a lot of potential with this and base a lot of it off the Superman: Brainiac graphic novel, which ends in tragedy for the Man of Steel. Who, know, maybe build Brainiac up for a future film. I personally would like that very much, but Superman has got quite a few very good rouges to make great stories out of, like Metallo or Parasite.
If it isn't done in Man of Steel, maybe in this explore Clark's longing to know the history of Krypton and of his biological parents and feels less isolated or longing in Kara.