The one thing I like about the Ultimate Universe (and there are very few things I'm liking about it these days) are that, when they work best, they all share a universe, and have a unifying undercurrent of major themes and motifs. That's what I'd like to see in 2099 - take the four major lines and extrapolate their central themes to the extreme.
We have a superhuman arms race, but the biggest threat to that are the mutants. With mutants around, any dirt poor country or group of crazies can cause devastating amounts of damage pretty much anywhere they want with the help of mutants. As a result, the United States becomes increasingly and rapidly more insular. Alternate power sources discovered by Reed Richards wean America off of foreign oil, and allow pretty much everything America needs to be produced internally. The borders are cut off completely, with defense devices created by Dr. Storm's think tank and the Ultimates cutting off the borders from everyone. American citizens are prohibited from traveling abroad, and citizenship is offered rarely and exclusively, only when petitioners have something amazing to offer the government. With all of America's defense internalized, S.H.I.E.L.D. eventually subsumes the rest of the military programs and accounts for the whole Defense Department. The Ultimates become legendary, the highest high of celebrities, and are gradually increased to serve as the standing army of the United States. Their sole purpose is to protect the United States from external threats and to provide defense in the rare cases where American interest is forced to venture beyond the mainland. The second arm of S.H.I.E.L.D. is the Sentinel Program, an intelligence agency that interfaces its agents like computers to monitor any and all mutant activity, and to combat the internal threats of gene manipulation. The only open government persecution is the fact that any and all mutants are subjected to complete surveillance. Meanwhile, public sentiments towards mutants are rapidly turning violent. Outside, the world is in chaos. With superhumans running rampant, regimes flip by the week. Each book would deal with a different facet of the universe.
Ultimates 2099: Captain America, who has yet to age a day, heads the Ultimates Intiative, the soul purpose of which is to combat external threats to America. Iron Man is the genomic makeup of Tony Stark patterned into AI. This AI conjointly operates the Triskelion (headquarters of the Ultimates), Stark Tower (headquarters of the Sentinel Program), and a veritable army of Iron Man soldiers. Thor is considered by some a god, and by some a madman, who governs over the territory of Scandinavia, which has become a series of small, earth-friendly communes.
Ultimate Spider-Man 2099: 15 year old Peter Parker wakes up in a laboratory with all his memories intact. An internal terror agency called HYDRA is operating within the United States, headed by a mysterious scientist with robotic arms. Using cloning technology that has been slowly perfected over the last 100 years, they are creating an army of clones to overthrow the United States government, clones with startling intelligence and superhuman ability, but all with the same genetic makeup, making their personalities predictable and tweakable. But something goes wrong, and Peter Parker finds he has to shoulder great responsibility and take down the organization. His only ally is the Black Widow, a deep undercover Sentinel agent using the code name of a long forgotten precursor.
Ultimate Fantastic Four 2099: After a fallout with the United States government over their methods, the Fantastic Four disappear into the N-Zone, to explore the unknown quantities of the universe. That is, until they fall back into the year 2099, barely aged, to find a world completely changed. With their vast experience, they have become near-gods, manifestations of the elements they represent. They venture into the savage world beyond America to try and find some way to fix the universe, and before all is said and done, they'll end up tangling with SHIELD.
Ultimate X-Men 2099: People sure hate mutants, yeah? Not quite sure where this one would go without it feeling like retreaded territory.