What I would do with Ultimates 3... off the top of my head...
The Ultimates are corporate sponsored and one line keeps ringing in my head. It's the line from Ghostbusters about how they had leave the school and go into the corporate sector. The Ultimates being corporate sponsored makes them a tad too similar to Ultimate X-Men for my liking. So to follow up on the Ghostbusters line and in an effort to make the Ultimates different from other line properties....the Ultimates becoming a company.
Hear me out.
Stark Industries is the Marvel equivalent to IBM/Microsoft and even with that combined money, the Ultimates would eat through funding like no one's business; collateral damage and lawsuits alone would cause Stark to loss millions. I also see lawsuits with SHIELD and the US government because these people are taking government sponsored tech and stealing it. Contracts were broken, and soldiers went AWOL. There will be a lot of trouble for these people due to their actions, and I doubt Fury and SHIELD will forgive easily.
So Tony Stark's a businessman, and sponsoring a super team with these troubles is bad business for Stark Industries, so the Ultimates need help elsewhere, but sponsors are hard to come by unless they have ulterior motives, so Tony does what he does best. He tries to make the Ultimates into something marketable.
The toy rights are still owned by the government, the uniforms might very well be owned by the government, and the movie and game deals would be in dispute. So all the Ultimates have that's marketable is themselves.
Tony suggests making the Ultimates a security team, maybe he uses the term "heroes for hire." The team doesn't like this (Offhand, Thor and Wasp wouldn't dig the idea at all. Clint, Wanda, and Pietro would go for it) and there's some infighting, but being independent means they need to offer services to get paid, and super sciences and soldiers who have been celebrities for years now and have saved the world three times...don't want to be garbage men to pay the bills.
Different groups and people sponsor the Ultimates, like Doom, the Worthington family, Hellfire Club, if OsCorp or Hammer Industries is left use one of them, but none of it is enough to afford the jets, weapons, upkeep, food, and keeping the Ultimates at their current pay rate. Tony gives in time and time again to pay the differences but he has a responsibility to Stark Industries and such actions are not taken lightly by its stock owners.
Salvation comes from a company called Williams Innovations, a weapons company that primarily sells weapons overseas since Stark supplies for SHIELD and most other countries. Williams Innovations will throw money at the Ultimates and return them to a world police like power with the ability to deploy anywhere there's a crisis under one condition: it's owner (Simon Williams) gets to become a member. They end up agreeing and thus we have Ultimate Wonder Man.
The Ultimates are properly funded again and do their Ultimate style fighting albeit with Wonder Man, a superhero junkie living out his dream. Wonder Man is decked out in tech which gives the illusion that he has powers. He's a geek for these heroes and he has a strong dislike for Tony Stark due to years of out selling his company, and more importantly, for being a hero before he got to be one.
Wonder Man runs the team into the ground, as you'd imagine he would. His decadent spending and reckless behavior would prove to be his company's undoing and the Ultimates would fall with it. They would blame Wonder Man and he'd blame them for these turns of events.
Stark is forced by his board to pull all funding or risk losing his position in his own company.
The Ultimates sell out to stay together and become mercenaries for an issue or so. Quicksilver patrols the boarder for illegals for some racist Texan militia group. Scarlett Witch is paid under the table for changing the probabilities to make a politician's popularity go up and win a reelection. Captain America's taken out of the team due to a lawsuit about the government owning the super soldier serum and the name "Captain America" he's left as being some rap star's body guard. Thor fund raises and preaches for the importance of having an independent Ultimates. Tony and Clint are hired to put down a small revolt in Latveria. Janet quits the team (she's wanted to in Vol 1, she left Steve in Vol 2...I don't see her staying around when things get tough.)
Infighting happens, as it always does with these people, and the Ultimates quit. Quicksilver and Wanda head for Europe. Steve gets a factory job. Tony goes back to Stark Industries. Thor goes back to his little church of the Odinson. Clint returns to the service, black ops. Wasp does commercials. The Ultimates are finally defeated by a lack of funds.
Simon Williams has been busy. His idols were mean to him and they ruined his life. He still owns his gear and rather than foolishly march into New York City looking for a fight, he sells his super gear to the highest bidder, moves out of the country, and gets his lifestyle back.
Terrorists with the Wonder Man tech do what they do. SHIELD tries to slap them down and even unleashes Mahr' Vehl, Vision, and Falcon. Avengers Assemble..yah de yah dee yah dah. Fight's over.
The Ultimates reunionite (surprise!) and agree to government sponsorship in exchange for more freedom than they had originally (think of the UXM after Millar's run).
I really think the Ultimates should be government sponsored. I liked it that way and if I wrote it they would revert to that way. There's still Ultimate stories to be told but without the government sponsored military angle...they're just basic team stories ala Justice League or Avengers.
I also think you can't top Ultimates 2's villains in sheer scale, there's no way. We still get a big battle somewhere (not New York or DC. Might as well mix it up) but we should focus on characters more for 12 issues and the difficulties of running a team and being in a team.
I also like having Wonder Man build up to be a stereotypical villain and then have him sell his tech. I always wondered why villains didn't just sell their goodies and forget about vengeance (who really seeks that anyway in real life?).
I also think getting the Ultimates back with SHIELD opens up the characters available for play. They have Vision, Falcon, Mahr Vehl, Betty, Fury, Hank, the money and power to hide Hulk, She-Hulk, Carol Danvers, and every SHIELD personnel you could want. Having them leave SHIELD cut the supporting cast down to nothing but Happy since Jarvis died.
Is my idea perfect? No. Just threw it together right here. I also thought about making the Ultimates into an allegory for the real life
Blackwater Worldwide but it would take more thought to figure out what to do with them once you've made them basically amoral mercs who work for governments after all the events of Ultimates 2.