I'm going to assume for the sake of the exercise, that the situation is similar to DC's plans, a soft relaunch that reboots various franchises on varying scales depending on the state of the property but generally focuses on a slightly younger universe. The one thing I liked about the Ultimate Universe that was never satisfactorily fleshed out was the underlying backdrop of a superhuman arms race. Ultimates dealt with the implications of superhumans on geopolitics; Spider-Man with the implications of multinational corporations having access to the technology; X-Men with the ethical questions of unregulated walking WMD's; and Fantastic Four with the socio-cultural effect of super science. So, this sort of backdrop would seep into the main universe instead. The Ultimate imprint would be shuttled or turned into a prestige line. Creator owned properties (like Criminal, Scarlet, Casanova, etc.) would remain separate, as would (obviously) licensed properties (Oz, The Stand, etc.). Some lines will largely remain the same, while others would get huge overhauls, as you'll see.
I'll be posting it in pieces, broken down by families of titles, since it's a lot of titles, and there's going to be some depth in the explanation.
The Avengers: Avengers teams and associated franchise characters, with a focus on accessibility to tie-in to film franchising.
1. The Avengers: In lieu of event titles, this would be the big, earth-shattering story hub, probably broken into volumes like the Ultimates was. A couple blockbuster stories a year starring Iron Man, Captain America, Thor, Wasp and Ant-Man, Hawkeye, and Black Widow. The first story would follow an origin, with the Hulk as the nemesis (setting up his book), before jumping forward six months or so and getting into the thick of it. The team is coordinated by Maria Hill, who reports directly to clandestine SHIELD director James "Bucky" Barnes (That's right. You'll see....).
2. Iron Man: Largely unchanged. There are a few keystone characters who are accepted as being around significantly longer than the recent superhuman boom, and he'd be one of them. Broke again, but brilliant and driven, Stark is out of the weapons game and looking to find a new model of business that averts the global crises looming over the modern age.
3. Captain America: Younger and more flawed. This is a Captain America that's only been out of deep freeze for a couple years. During WWII, his adventures were largely PR, with the military brass wanting to preserve their last human subject of the super soldier formula. He spent most of his time chaperoned by his badass normal sixteen year old bodyguard Bucky Barnes and disappeared in a last act of heroism. Now he's back in the world, uncomfortable and uncertain in the way news reels and decades of propaganda have lionized him in the public eye. He's on retainer to SHIELD now, trying to live up to the legend he never really was.
4. Thor: Donald Blake is the head psychiatrist at Vegas General, a dank and underfunded sub-basement of the hospital proper. He lost his wife and son in a car crash a year ago and hasn't managed to crawl out of the depression since, stuck with a cane and a dependency on alcohol and prescription drugs. His life is dull and gray, his sleep haunted by vivid dreams where he's Thor, son of Odin, fighting a war on the precipice of armageddon. Sometimes he feels like the real world is just a lie and this is the only truth. Then patients start appearing who reaffirm his delusions. A fat man who suffers from pica, eating anything around him despite its edibility; a young man too paralyzed to make any decisions at all, paralyzed by the belief he will bring about the end of the world; a woman found near catatonic, found severely burned and walking nude through the desert, clutching a butcher's knife. Donald becomes obsessed with her resemblance to his dead wife. Then there's Lois Keegan, rare weapons collector and ruthless hedonist owner of Yggdrassil, Vegas' hottest new attraction, a Nordic themed casino with an enormous tree rising through the center. The shared delusions of his patients suggest to Blake that there was a war in heaven, and the gods were cast from heaven, minds broken, in human bodies..... Is it true, or is he just feeding his own psychoses?
5. Avengers Institute: Avengers Academy, but bigger. Kids with powers are offered training, protection, and education grants in return for a four year commitment to the armed forces. Instead of training the kids to be out and out superheroes, the primary focus of deans Hank Pym and Janet Van Dyne is to find the kids a productive role in the future of America. More often than not, it's to find a creative use in civilian occupations, rather than as superheroes proper.
6. The Incredible Hulk: Bruce Banner washes ashore the island of Malta, his memory lost, taken in by an isolated nunnery. That doesn't turn out well for him. When men come for Bruce, the nunnery is in shambles and he's forced to the continent for their sake. Here, the news are only talking about one thing: his death, the act that led to the formation of the world's first superhero team. And despite the entire world thinking he's dead, it seems everyone is on Bruce's trail: terror groups, world governments, intelligence agencies, mercenaries. It's The Fugitive! But international! And he turns into a mindless, destructive green monster! Poor Bruce just wants to be left alone....
7. Avengers Next: In a bleak future, the children of the original Avengers are forced to challenge their own code of ethics to keep the world together. How did things get so wrong, and why are they required to pay for the sins of their fathers? The mysterious state of affairs can be used as fore(post?)shadowing for epic present day Avengers adventures!
The Initiative. I don't think I'd have a federal mandated 50 state initiative, but this is creatively the same idea: teams and characters who represent the United States outside the typical New York City crowd.
8. Runaways: They never played much in the greater MU and they'd remain unchanged, their history intact: kids who's parents were super-villains, still trying to figure out what they want to be, and avoiding the superhero lifestyle. So they move to Seattle, the golden land of liberals and rain, where things are quiet. Unfortunately, criminal entrepreneur had the same idea, moving his family to Seattle to create his criminal empire. He's funded by his mistress, wealthy and ambitious criminal/magnate Whitney Frost (Madame Masque). BKV's two great Marvel creations go head to head!
9. Single Green Female Lawyer: Reserved but intelligent and impassioned Jen Waters was Atlanta's young wunderkid ADA. But a horrible car crash and a blood transfusion from her cousin left her with the power to turn into THE INCREDIBLE SHE-HULK! It destroyed her career in the judicial system but opened up new doors. She now stars in the popular network primetime dramedy Single Green Female Lawyer. Many of her coworkers are wannabe "celebrity heroes", looking to make their names known so they can step into a lucrative career in the Hollywood superhero merchandising circuit (Superhero movies are big business!). Her best friend is Patsy "Hellcat" Walker, a former actress turned cynical who now makes a living in costume, making appearances at genre/auto conventions and business grand openings. And somehow Jen finds the time to mentor a group of misfit teens who call themselves "The Young Allies". Glib, tongue-in-cheek commentary of celebrity and superhero/television culture.
10. Moon Knight: LA's dark avenger! He was a mercenary with a unique knack for reading people. Now bonded with the spirit khonsu, he's found a new use for his observation. He can take on the personas and specialties of the people he's studied, sifting through his closet of personalities to find the right specialties for the job. Unfortunately, they aren't always content to just linger beneath the surface. He's probably still a producer for a ****ty syndicated action-adventure show.
11. Thunderbolts: would largely stay the same, but I'd probably move them to Wyoming or Montana or somewhere. It doesn't make sense to me that they'd keep the most dangerous superhuman federal prison off the coast of New York, so instead some quiet, forgettable state in the middle of nowhere holds the world's most dangerous prison in return for a big federal boost to their coffers.
Spider-Man. Okay. This is easy.
12. Amazing Spider-Man: He already got a reboot so we're leaving him untouched. His history's intact, though probably not the Avengers stuff. In NuMarvel, he's the world's first vigilante hero, and so he's been around a while.
13. Venom: 'cuz he sells books. Let Remender keep it.
14. Front Line: Norah Winters, Jessica Jones, Ben Urich, and creepy little Phil Urich are the core crew of the Daily Planet, a newspaper that isn't afraid to get in the thick of superhero brawls and issues, keeping those guys honest and insuring the truth doesn't get lost. They frequently run into Damage Control, who handles the clean-up and investigation of these big throwdowns. Norah's main squeeze, Robbie Robertson Jr. (is that his name?) works for DC, and his dad is their boss. Rock.