Alright, so, ideas.
So, if I plotted it out, here's how the general history would roll out. The Legacy Project would be a virus that triggers the element causing mutation in the human body. The idea would be to have strains of different strengths. Lighter strains would merely trigger the mutation in the body of the human, making it possible to cheaply create an independent mutant army. Stronger strains would trigger mutation and then force it out of control, until (most of) the victims are either physically killed by the mutation, or forced into psychosis from the overload of the sudden and rapid exposure to the virus. The death rate for the virus is less than 30% but the damage done by spontaneous mutations multiplies those deaths and adds an extra chaos to the scene. The man with the plan would be Apocalypse, a mutant terrorist from Egypt who claims to be born at the creation of the earth, and who only appears publicly or in the media behind huge and imposing looking armor. The attack is unified in that it's fought simultaneously on practically every continent. Europe, Asia, and Africa are savaged. The Americas manage to survive generally unscathed, due to the development of the SHIELD cure for the Legacy Virus. While they don't have a chance to get any help out to the other continents, the US manages to stymie any catastrophic disasters within the states, and manages to contain the attacks throughout Canada and South America to particular areas. The United States quickly goes onto the defense. The rest of the world is considered "under quarantine" and all flights and boats in and out of the country are cut off. Shortly thereafter, about half of the South/Central American countries and all of Canada begrudgingly cede to the United States, out of need for a unified front (by the time of 2099, all of South and Central America except for a few hot spots have been forcibly taken under control). The idea here is to take Millar's political tilt in the Ultimates and twist it a little. The New United States is still the one global superpower, but here it's forced to be aggressively defensive instead of just outright aggressive. It would also be an interesting twist for the Cap/Thor/Stark triumvirate. Apocalypse would be trying to initiate the next evolution by forcing everyone to involve and building an empire out of the wreckage. He would use devoted followers and the remnants of HYDRA (who would turn out to be the criminal terrorist organization who primarily funded the attacks by the Liberators) to launch his plan into motion. His Horsemen would be generals, picked from major players within the organization. By the time 2099 rolls around, many of them would have passed their dynasty on to ancestors. Maybe the Mandarin and his powers are a title and dynasty, rather than just a supervillain name.
Apocalypse claims the Middle East as his throne of power. Alexandria is renamed Apokolips (Okay. Maybe not). He insists that the Age of Apocalypse is totally on. He's so right. The rest of his lands are consolidated between his Four Horsemen (one of which I figure would be the Mandarin, to twist the Stark/Mandarin feud and making it an international military feud). Ultimate Fin Fang Foom would be involved in this plot, also. In the New USA, Reed Richards, his family/team, and the kids underneath Nevada are conscripted to head the New United States Defense Project. Doctor Doom returns to find Richards missing (government protection) and his kingdom in disrepair. Without Reed Richards there to distract his attentions, he manages to fashion Latveria into a well-maintained, if mildly oppressive techno-magical empire, which stretches through the Balkans.
As for USM 2099...
When SHIELD wrested control of the US, the structure of the complex completely changed. The CIA has taken a considerably larger role (and probably a more sinister name, but I can't think of one now), most of which was wrested forcibly by the late Doctor Otto Octavius. So the CIA drops off the face of the map. Huge chunks of government funding go into it, but seemingly nothing comes out. Dr. Otto Octavius is at some point replaced, and then replaced again, then a third time, each by people who carry his name. They're rarely seen. The reason why is, they're building clones, creating identities for them, and sending them out into the world for various intelligence purposes. The problem is, the researchers discover that for some reason, Parker's genetic material is the only source of DNA that can be cloned with a large amount of effectiveness. So, they keep producing all of these clones of Peter Parker's DNA - sometimes with powers, sometimes without, sometimes with different powers spliced in - that are each tweaked with to look and operate different (They're all not exact clones of Parker, but they're all derived from the same DNA base). Except, Doctor Octopus is shaving a few extra clones off the inventory and using them for its own purposes. Octopus has managed to install Parker clones in major positions of power throughout the United States.
Speaking of the doctor - I'd try to explain away the old magnetic powers. My angle is that Doc Octopus made his claws out of vibranium - a metal that sympathetically responds to nearby thoughts. With the right technology, he figured he could calibrate this technology to his nervous system, and the metal would respond to his thoughts, acting as tools. It worked a little too well. The vibranium responding strongly to his thoughts, becoming dead obsessed with scientific curiousity. It would regularly operate either on its own, or with Octopus unconscious, on upgrades to its equipment. The magnetic field control was one. Another was a sort of battery pack that allowed him to operate independently for a short time while it tries to find a host. It's now on its fourth body, and she's a hot chick. She's also way corporate evil. I'd twist the design of the tentacles, making them pliable nano-machines that comes from a disc grafted in place of several vertebrae.
So, out in the middle of this crazy 2099 world, a kid wakes up with Peter Parker's memories. He's been liberated from the clone tanks by an agent of HYDRA, who names herself after the legendary Black Widow. HYDRA in the United States has evolved into a sort of liberationist guerilla movement with violent tendencies. Anyway, our boy has all the memories of Peter Parker up to about 16 tears old, and he's thrown right in the middle of this dystopian future. You'd have to stick with the same old theme of great power/great responsibility. Whether he needs to be responsible to the moral compass of a teenager from a hundred years ago, or if he's responsible to the agency that created him, or the terrorists who saved him from becoming another drone. And right on the heels of that, he finds out that Peter Parker (who unmasked as Spider-Man) and Spidey himself are both huge counter-culture or teen icons, in the same way as Che Guevara or Kurt Cobain or maybe even Malcolm X. Spider-Man is a hero to the disenfranchised. An early story would have him breaking in to a Spider-Man museum to take a costume for himself, from somewhere later in Spider-Man's career.
The main plot would follow Spidey as he tries to unravel the new Doctor Octopus' fans, and have him becoming a huge hero to the general public, but a threat to both the CIA (who are planning on consuming SHIELD) and SHIELD. Carnage Mk IX would be a highly sophisticated evolution of the original Carnage created by Curt Conners. It's a highly adaptive, mobile, and destructive weapon that can annihilate a city block in moments that becomes stronger when stirred into frenzy, and is believed to actually initiate hallucinogens in the surrounding area, at the height of this frenzy. VENOM would be special police units run by SHIELD and operating as a futuristic SWAT team. I remember a really bad Venom storyline from back in the day (Separation Anxiety, maybe it was called?). From what I can recall, there were a bunch of symbiotes that split off of Venom, or Carnage, or someone, and they formed their own personalities. I also believe there was a team of hunters on Venom's trail who each had a justice gimmick. They all had silly court names. The Venom unit would be an ultimization of both of these ideas. The unit would be highly trained police officers with high-grade equipment (and silly themes and code names) who can activate symbiotes to take down larger threats. The symbiote of each character would synch up to the different symbiotes in that awful, awful story. Oz has become an illegal street drug, popular among criminals for the physical boosts it gives you. A gang called the Goblins pops up, with a whole subculture of goblin-esque body modification and heavy use of the drug. Hierarchy is determined in part by who's been made most grotesque by the Oz. Maybe there'd be a civilization of lizard men in the sewers, spawned by Curt Conners. But there'd definitely be a new Ultimate Knights - a bunch of freedom fighter punk kids who try to fight corporate oppression in the city. Mayday Parker (AKA, The Amazing Spider Girl) claims to be the great grand-daughter of Peter Parker. Daredevil would be a riff on the Universe X version. He can suffer any form of injury and survive. He makes his living as a street performer during the day. The great grandson of Wong, who claims he attended by Doctor Strange before the Sorcerer Supreme left for other worlds, would be the team's magician. There'd also be a Scarlet Spider, maybe. Perhaps he could be a clone implanted in the team by Doc Ock.
