Director - Me.
Screenwriter - John Byrne
Supes/Clark - unknown that recalls the art of Byrne in the man of steel GN
Lex - give the guy a rest. using the same villian over and over I feel has been a real drag on the Superman movies. If he is used, do not make him the main protagonist. Use the billionaire industrialist version of the character in a B plot.
Lois - Ann Hathaway?
Darkseid - Michael Clarke Duncan. though this may be a little too hollywood/typecasting
Brainiac - Paul Bettany
Doomsday - CGI? like The Hulk?
I would do a trilogy with Darkseid as the overarcing villain.
First movie Darkseid is seen only as the motivator behind Brainiac finding Superman on earth. Not even Brainiac would be aware of the manipulation. Superman has to take on Brainiac.
Second movie Darkseid continues his manipulation by secretly letting Doomsday escape Cadmus. Superman fights to stop Doomsday but seems to die in the effort at the end. Epilogue scene of the some/all of the "reign of supermen" characters being seen in Metropolis.
Third movie, Darkseid invades. This movie starts with the "supermen" and maybe a few guest JLA members dealing with the invasion. Superman himself would not fully return till the midpoint of the movie. There would be small cut scenes of his "return" before this. I invision a scene where the invasion has reached it's darkest point and Darkseid is giving his monologue in the ruins of Metropolis. Closeup of Darkseid from the back from the shoulders up. A hand reaches into frame and taps him on the shoulder, "who!?!", as he turns. The flames of hell burning in his eyes. POW!!!!!! Darkseid goes sailing from the classic right hook. Camera switches to reveal Superman in all his glory, grim determination on his face. "No one does this to Metropolis. Not on my watch.". The battle is on!!!