Your basic speculation thread, but focused on independent storylines from both franchises you'd like to see in the series: Death in the Family- The original story does include both heroes, and adapting this story in a Batman/Superman movie would allow the, to circumvent the whole "Why doesn't Superman help Batman" thing. It'd need an update and probably a better overall plot to keep Superman involved. If they were to feature some kind of Joker/Luthor team up, this would be the way to make sure the antagonists live up to their potential. Imagine watching the movie where Robin dies and we see Superman's anguish at failing his friend. Heck, you could even through in Supergirl and tease her death from COIE before pulling the bait-and-switch. Search for Lois Lane- the story where Lois was kidnapped for weeks and Superman had to call in Batman to find her while suffering from kryptonite poisoning. I don't necessarily need the poisoning story, but seeing Batman actually do something Superman can't and analyze how gritty and frightening his world is in comparison will just about justify any team-up between the two. However, I feel there does need to be an element of trust between the two before this scene happens, so it's definitely sequel material.