I've said this before and i know it sounds like a broken record - but i would love MOS2 to be set weeks, yes weeks, after MOS.
In reality, we had what 18 months between MOS and BvS where we know absolutely nothing... it's practically a clean slate, what happened, what rescues did he do, how was the city with him there, did he save a cat out a tree.... and all we know in that time is that at some point, 'lex luthor' got pissed off as his dad vanished, started to track meta humans and set up a war between bruce and clark. That the people of the city were mainly for him, but a few against.
Get the crew back, focus on new employee 'reporter clark' and his secret floosey lois. How does he adjust to workign there, what does he do, let's build the clark kent character up through the eyes of his collegues. We get to define him.
Same goes for superman, we see him helping rebuilding the city, darting down and helping construction crew - show off his powers, him working and befriending people, making the city his home - focus way more on kids and the positivity he brings.
Let's see lois and clark investigating that leads them into hot water that superman 'saves' the day. Let's see him back at smallville with lois, old friend lana pops up.
New interm 'jimmy' at the planet.
The big bad - lex luthor snr - he is exposed and has to go on the run, obviously perry forbids the story going public as luthor snr has too many friends in high places, think of it like Epstein, when he was arrested and put in jail but only served like one day a week for a year and the media buried it..
Make a superman story where lois and clark and the city are the heart, with action spread out in the form of superman. The final act could be like a heist.
So we have re-established everything and sueprman seems way more positive - then the story continues with BvS, JL but they are more side stories. Then, MOS3 is set now, after the events mentioned and we have a clean slate.
Aquaman wasn't hurt by BvS or JL, Shazam too, WW the movies are set in the past... Blackwidow same thing and she is dead, that's how i would continue with Cavill so that there is a seperate MOS1,2,3.