Having Superman lose is basically one step short of killing him, and many are saying the Death of Superman is one they'd like to see in the films. I personally don't need that, losing to Darkseid would be perfect, maybe it's not a loss as much as Superman escapes from the fight with neither winning or losing.
This is all MOS3 speculation
I'd like it to see Darkseid basically decide not to kill Superman in order to make an example of him among the Earthlings. This is different from the movie version of Bane.
It'd be great if he told the people of Earth that their hero figure is weak, and that he will ultimate enslave them all. Superman gets up for one final encounter grabbing onto Darksied's throat, but Darkseid knocks him back, opens the Boom Tube and escapes, laughing all the way.
Superman looks out at the people of earth with tears in his eyes, and tells them that he failed. I wouldn't mind the people of Earth realizing that this might be their last day alive, and so they help each other out and embrace the character and ideals of Superman (thus closing out the trilogy thematically).
And even though the 'story' of Superman is TECHNICALLY over, the film should end with a tease with Wonder Woman, or with Superman, Batman, and Wonder Woman setting up the JLA movie near the end to confront the possibility of Darkseid's return.
I would like it to be a subversion, in which it turns out the threat is unexpected, and NOT related to Darkseid.
If there's a separate JL trilogy, I'd want it to END with Earth being invaded, and Superman pretty much killing Darkseid near the end. Okay, I want that "World of Cardboard moment." I won't lie.
As for Doomsday, the Justice League would have to be set up for Superman to realize that he can't risk the members of the League for this foe. I'd want Doomsday to be a "secret weapon" that Superman sacrifices himself to.
Otherwise, I don't really want the character in the film.