The movie would be borderline animation, and black and white like Sin City with only things like Superman's suit in color (but graphic flat shading).
The whole comic book look of the film would allow for special effects to better fit in. The flying for example would be easier to make look real.
The following isn't in color, but it let's you know where I'd go with the casting and cutting the suit. I want the cape to go over the shoulders; I want a Roman look. And when he dies at the end of the first movie I want a flush S on the cape so it can be draped over the casket in the closing scene.
So the story is simple. A trilogy with Darkseid as the macro villain, Superman is in his 80s, he isn't the same man anymore, he is alone and dying, Luthor killed Lois long ago, and Superman killed Luthor.
The Donner footage of Jor El would be used as well as the old music score, but that is all. I am undecided as to who to cast as Darkseid. He can't look generic.
In the first film Darkseid comes to Earth and plans to make a martyr of Superman so he can create an inorganic clone of him and use the resurrected image to use Earth's own mythologies against them (tricking Earth into giving up their independence to Darkseid's false Christ puppet). He doesn't come with an army; he only comes to kill Earth's greatest champion. He unleashes his living weapon bound in a green silk called Gleipnir which grows tighter the more one struggles; no name is given to the creature (the final chapter of the film simply shows a title reading Doomsday like a Terantino film).
http://img.photobucket.com/albums/v695/nemo_83/doomsday.jpg
Doomsday is composed of white diamonds (a side effect of all the presure from struggling in the bindings) and would have a power not seen in the comics; he would somewhat control the earth (think Sandman from Spiderman). I don't know who to cast for that character either.
The first characters to face Doomsday would be Swamp Thing and the Martian. The Martian would have the iconic cape but the coloring would be different and the make up would be Giger-esque, much liberty taken in the design as with Mystique in Xmen.
Shazam would also appear; the actor would have to have the squarest jaw line and the white cape should be more like a scarf.
The first hero to appear other than Superman in the overall film would be the Dark Knight in black and white.
The first time we see Batman, he would be trying to be slick sneaking up on Superman (who of course calls him out); the purpose of the meeting being to bust up a bunch of gangsters. Joker has a new group of super soldier mercenaries led by Bane (everyone has guns including Batman except for Superman). In the mix as well in this chapter of the film would be the following vengeance seeker:
In the final fight, Doomsday and Superman break a lot of stuff, and Superman uses a couple of things like a steel post as a weapon hitting Doomsday like a baseball into the air reaching for the canope of the skyscrapper skyline. In the end the beast is defeated by Superman who has a Mad Max Beyond Thunderdome moment feeling pity for Darkseid's prisoner and does not kill it. Darkseid retrieves his weapon and the cybernetic silk envelopes him. Superman is weak but he fights Darkseid atop the ship's open throne room as it goes into orbit. At this point he loses his cape which drifts to the ground (and is draped over an empty casket in the burial scene in the end). Superman grows weaker and dies, freezing quickly in the cold of space seated on the throne (after being thrown into it by Darkseid). Darkseid transmits the images of the frozen Superman to Earth and departs.
Superman's DNA is harvested to create a clone which is sent back to Earth in part two to govern the planet through martial law in Darkseid's absence. Superman's body is to be destroyed; Darkseid has the throne ship with Superman still seated there launched in the direction of a blue dwarf. His body thaws and is super charged from the exposure, he awakens fourty years younger, and filled with a whole new power that lasts the duration of the trilogy.
Superman returns to Earth piloting Darkseid's towering prison where the Green Lantern, Wonder Woman, Batman, and others have all failed to defeat the Man of Steel. Kal El digs up his cape and then proceeds to kill the jebus out of a clone.
In part three Superman goes to the home world of Darkseid, unleashes Doomsday, faces Darkseid, and destroys him freeing the peoples of many worlds from the self proclaimed New God.