That's a pretty good one, and I like that Terrific, Mid-Nite and the Atom are the last ones standing, basically.
Here's the full version of my idea for a Superman run:
I've noticed that, for a while now, Superman's stories have been in a rut: He flies around the city, some weird sci-fi leftover from the B13 virus or one of Metropolis' hundreds of mentally deranged vagrants with access to vaguely futuristic technology starts causing trouble. Meanwhile, he's going through some kind of trouble at the Planet, be it some upstart reporter vying for his job, a story that would help bring down some corrupt fatcat or otherwise help the city that isn't getting anywhere, or something like that. He asks for Lois' or Ma and Pa's advice on one or both of these matters, and then he comes up with some solution, either wrapping things up that issue or taking a few to complete.
My idea is to start from the angle that the reason the comics are in a rut is because Clark's life is in a rut. He's fallen into a pattern. A daily formula with minor variations depending on the situation. And you know what? He's fine with that. Clark's always been a simple guy. Not that he's uninteligent, but he likes things to be simple. Likes things to be quiet and to run smoothly. In the weirdness of his life, the formula makes him comfortable. So, the first couple of issues of my Superman run would be fairly standard. **** goes down and he handles it in the tights, right alongside **** in the office. That'll last for maybe five or six issues.
But then, something would happen that would stand as a testiment to one very simple truth: Sometimes life deviates from the formula very abruptly.
During one of the early, standard issues, there would be a few instances where Lois tries to talk to him during the day, but either work or his Supermaning keeps him too busy to listen. At the end of the day, everything's fine and the city is safe, and Clark has enough time to listen to Lois tell him that she's pregnant. Going from there, their first question is "how is this possible?" They are told by some scientist, perhaps Mr. Terrific and Dr. Midnight (I must say, I absolutely adore that pair), that it simply isn't. But it happened anyway. It is the very definition of a miracle.
Meanwhile, and this would start in the second or third issue, during the standard stuff, to keep things interesting, we see Lex on the run. He realizes that his sanity has been slowly deteriorating ever since his impeachment, culminating in the seemingly random killings of his Everymen and his rampage in Metropolis. His obsession with his rivalry with Superman has led to him developing severe paranoia and violent moodswings, to a point that borders on DID. He goes on a sojurn of sorts across the country to face himself so he can once again face the world, as well as build up resources and manpower. He ends up meeting a genius college student who wishes to become a mad scientist, and she acompanies him on his quest.
Clark is trying to adjust to becoming a father, so much of the next few issues will be more talking heads style. Not much action, more character stuff. There'd also be a sub plot about a new mobster in Metropolis that would slowly grow in importance. Lex finds inner peace, and begins to atempt his old goal of saving th world from itself anew, this time forming a team akin to The Authority or The Elite (possibly even a new incarnation of The Elite). He also remembers something that had been taken from his mind: Superman's secret identity. They start operating much like The Authority, hitting the corruption of the world with no regard for the law and a very totalitarian aditude. Lex begins wearing a suit akin to what h wears in Justice. Eventually, Lex starts going after the mobster in Metropolis, who is revealed to be The Parasite in disguise. Able to sense that Lois is pregnant when they come face to face, he tries to use that against Superman, resulting in a direct confrontation. This teaches Clark that his responsibility is no longer just saving lives. He's not got a family to protect. Rudy gets away and Lex kidnaps and brainwashes him for his own ends.
Lex's team become major figures in world affairs, with Lex becoming a sort of outlaw celebrity, hated by many and loved by others. He starts stealing advanced alien technology from the government and sharing it with the Earth, and publicly criticises the government and the super heroes of the world for hording all of the wonders in the world for themselves. He also begins killing third world dictators and taking over. This comes to a climax when he takes control of the U.N. and the White House and starts declaring himself and his team as the new world rulers.
Lex then sends Parasite and a newly hired Metallo to Clark Kent's apartment to beat him into a coma as he poses a threat to Lex's new world order. He then uses the adresses in Clark's apartment to take out other League members and other potential threats. When Clark is in his coma, he has a sort of near death experience where he talks with Mxyzptlk about what's going on with Lex, and his life in general. Naturally, Ray Palmer, who's been able to evade Lex's detection, works with Dr. Midnight, Mr. Terrific, and Steel to save Clark's life and revive him. That group then opposes Lex and end up stopping him, in a massive fight scene in New York to rival the last two issues of The Ultimates (they'd also be on time). Lex is arrested.
The next few issues are about the aftermath of Lex's coup. Clean up, reconstruction, and trying to bring stability back to the world governments. The next issue covers Lex's trial. At the end, the sentence is death by firing squad. Mxy starts apearing during his dreams, offering advice in regards to the changes in his life. We then see Lex's exicution, held in Metropolis at his request. There's no daring escape or door left open for a clever retcon. The gaurd puts a black bag over his head, and a firing squad ventilates his chest.
Clark, shaken by the recent happenings with Lex, and at a loss as to how to deal with raising a potentially super powered child and protecting his family from everyone who might want to hurt the kid, turns to ma and Pa. But for the first time in a while, they can't help him. This is a situation unique to Clark, and he has to figure out how to deal with it on his own. Mxy apears to him again, and offers a "tour of the office" while they talk. Going on a makeshift vision quest, Mxy breifly explains the nature of things while giving Clark what he really needs: Advice. In the afterlife, Clark speaks with Connor and gains a bit of closure with that (part of his fathership anxieties was him worrying that he'd fail his kid like he failed Connor). He even burries the hatchet with Lex, who's still trying to figure out where to go. Lex says, looking back, that their rivalry was so immature, and neither of them had any real reason to hate each other. Lex then says that he's considering reincarnation, leaving the door open for a clever writer to bring him back in some fashion. Clark then goes on to finally really meat Jor-El, speak with a few supernatural beings, and comes back a bit wiser and more confidant.
The next few issues are rather filler, dealing with more standard supervillain crap. Would probably have him fight The Silver Banshee or Riot, just for kicks. This is all building up to the Christmas issue, where the baby, a boy they name James, is born. Thus, the pregnancy was a Christmas miracle. The next few issues is more lighthearted than the rest of the run, with Lois and Clark adjusting to paranthood.
The final issue of the run has several jumps several years in the future. One has James being about seven, with Clark talking to him about how much of a miracle he is, and how his powers might manifest in the future. The next has James in his teen years, dealing with standard teen crap, until his powers finally manifest when he jumps in the air and only keeps going up. The finally bit has James as a young adult, wandering the world and using his powers in secret as his father did many years before. It ends with James deciding that it's time to go home to "take a crack at the family buisness." He's last seen with a sketchpad in his hand with a crude depiction of a costume partially isnpired by Connor Kent's many looks.
An interesting note is that, while the reincarnation bit would be, for the editors, a way of letting the next writer bring lex back, it would be strongly implied through his inteligence, mannerisms, vocabulary, and political veiws that James is in fact the reincarnation of Lex.
As for the members of Lex's team:
Metallo: Lex payed him, as well as promising him the chance to kill Superman.
Parasite: Kidnapped and brainwashed him.
Bizarro: Lex manipulated his limited intelligence and desire to be a hero.
Atomic Skull: Lex manipulated his fragile mental state and desire to be a hero.
Menagerie: Sister of the origional and former member of the Justice League Elite.
Plus a few new characters Lex created.