First of all, a summary of my personal beliefs about the series:
* the maxi-series format is cool with me, as long as it ships on time.
* Loeb's intention to make it read like a more traditional hero-oriented book is not necessarily at odds with the need to make it feel 'Ultimate'; it just demands more creative thinking, with regards to how the stories play out. Actually, Justice League Unlimited is a great model for this approach, balancing more 'adult/mature' ethical and moral themes with classic superhero action.
Given the chance to write Ultimates 3, I'd structure it this way:
"Disassembled" (#1)
Six months after Ultimates 2 ends. The series would open in the midst of a mission. The current line-up of the Ultimates are raiding the headquarters of Fenris International (from UXM's "Cry Wolf" arc), which has since relocated from New York City to Austin, Texas. No explanation is given to readers for the attack, other than that the group is a front organization for funding mutant terrorist activities in the U.S.
The Ultimates roster seen in the battle is Cap, Hawkeye, Scarlet Witch, and Quicksilver. Meanwhile, (the original, female) Vision is coordinating the group's activities, from a mobile command center aboard a SHIELD helicarrier. While the others fight off the "Wolf Pack" guards, Cap succeeds at battling his way into the main offices where Andrea and Andreas von Strucker are hiding out. Before the Struckers can make skin contact and use their powers, Wasp flies out of a chamber in Cap's backpack, suprising Andrea with her sting. Cap and Wasp quickly take out the Struckers.
The next few scenes are on board the SHIELD helicarrier above New York. The city is obviously in the process of rebuilding (including a restored Triskelion).
By way of a debriefing and situation report, it is established that Iron Man has grown distrustful of Nick Fury and SHIELD, and Stark has ended all contracts with them. They are now monitoring his actions closely, but they have no doubt some of his work has slipped under their radars, given the extent of his resources.
It is implied that Fury let Bruce Banner go, and he remains a fugitive on the run from other authorities. Fury may or may not know where to locate Banner, if needed.
Hank Pym is missing in action, but SHIELD has seized whatever known assets he has, including the ant-control helmet and apparatus, as well as the schematics for Ultron and Vision II.
Quicksilver and Scarlet Witch admit (however begrudgingly) that they seem to have found 'their place' among the Ultimates, no matter how unlikely, given the respect with which they are now treated, after their involvement in the Battle for America. More crucially, they need the diplomatic immunity conferred onto them, to avoid facing up to their past as mutant terrorists, hence their decision to remain with the group. Furthermore, Wanda seems to have developed an unlikely (more than platonic?) relationship with the female Vision; she seems to have established the same degree of intimacy with the robot that she once had with Pietro.
Cap remains loyal but criticial, serving as a voice of reason, despite any misgivings he may have about the way SHIELD runs the group.
And Wasp loves the fame too much to risk a career move, at this point. Her relationship with Cap remains dedicated, in spite of past squabbles.
Hawkeye is a devout career man, and will not so quickly abandon his old pal, Fury.
Thor has decided to pursue his own individual interests, seperate from the group that he doubted, from the very beginning.
In the last scene of the first issue, we see Tony Stark presiding over a meeting at the Stark Enterprises Compound in Los Angeles. Despite the sinister mood of the scene, Tony himself appears to be in high spirits, and declares that "the big day" happens the following week.
"Force Works", "West Coast", "New", "The Crossing" (first arc, lasting through #S 2 - 5)
Tony Stark unveils Force Works, a team of superpowered individuals, organized right under SHIELD's nose. They will operate under the auspices of Stark Enterprises (similar to WildC.A.T.S. v. 3.0). The line-up includes Iron Man, Mahr Vell (from the Ultimate Galactus storylines), Misty Knight, Hawk-Owl (from Ultimate Adventures), Doctor Strange (from USM), and Psylocke (from the "World Tour" storyline in UXM; she joins Stark because her "S.T.R.I.K.E. project was absorbed into the European Defense Initiative" by her "******* brother"). Their physical appearance (uniforms, colors, etc.) deliberately suggests a resemblance to the original Authority (Psylocke = Jenny Sparks, Dr. Strange = The Doctor, Mahr Vell = Apollo, Hawk-Owl = Midnighter, etc.)
They were able to organize themselves without SHIELD's knowledge, by operating in a pocket dimension accessed by Strange.
Force Works stops an attack by the U-Foes in Hawaii (never explicitly named as such, but it's obvious).
Fury meets with the Ultimates to decide how to respond to this latest challenge; Betty Ross' involvement is key; the Ultimates need to "rebrand" themselves.
Basically, Force Works and the Ultimates compete for favorable public opinion, which means that Fury can no longer use his group for questionable black-ops style work.
He brings in a new undercover agent: Ronin. Ronin is later revealed to be Hank Pym, whom Fury has spared, in exchange for his services.
"Young Ultimates" (stand-alone story in #6)
A Fury solo story. Fury is alarmed to learn about a travelling group of young vigilantes in the MidWest/Great Lakes area, calling themselves the "Young Ultimates". He dispatches SHIELD Agent Sharon Carter to learn more about them.
She discovers that three of them have no real superpowers. Night Thrasher is just a fanboy with military surplus grade battle armor and a souped-up Segway. Speedball is an extremely talented gymnast and martial artist, with an incurable addiction to danger. And Namorita is an amateur Atlantis scholar with a set of glorified, arm-mounted water cannons that shoot propulsive blasts of dirty water.
However, Firestar is a genuinely powerful pyrokinetic mutant. Carter agrees to let SHIELD turn a blind eye to their activities, as long as they cease and desist immediately, and Firestar/Angelica Jones agrees to be trained as a black-ops agent for the real Ultimates.
"Hydra" (final arc, lasting through #s 7 - 12)
Fury learns that Fenris were just an influential pro-mutant break-away oragnization from a more dangerous threat: HYDRA.
HYDRA manipulates the individual members of the Ultimates and Force Works to compete for pieces of glorified doomsday device, in a storyline that reads like an Ultimized version of the "Avengers-Defenders War". Eventually, Tony figures out what's going on, and the groups coordinate a strike against HYDRA using both conventional superheroics and corporate manipulation (to cut off its funding, so that it can't organize the various command cells that serve as its many heads).