So basically, the original post says "Don't do the Ultimates because audience won't like a hero as the villain'?
So don't make Hulk or Black widow a villain. Zing! Skip the first book and go to the alien invasion story.
Seriously, it's not that hard. And if you don't like the way the heroes personalities are presented in the Ultimates, just use the 616 personalities. Zing!
None of that means that you can't use the storyline from the Ultimates:
Government agency SHIELD and their leader Nick Fury recruit superheroes to defend the country against a rising extra-terrestrial and supervillain threat. They take on an invading alien force that has ties to Captain America's past, and defend the city against a united front comprised of the teams most powerful enemies. (Obviously not in the same film, but aliens in the first, something else for #2, and all the villains for the sequel)
Even better, we could still have the team fight the hulk without turning him into the bad guy. The leader was set-up at the end of TIH, right? There's no reason he couldn't be a part of the villain team and mind control Hulk to act against the avengers. They fight. Hulk would eventually break his hold somehow and rejoin the good guys for the big final fight.
At the end, have them disconnect from SHIELD so they can help the world without making it seem like govt. intervention, and then that frees you up to bring in more 616 elements (ie, other heroes, villains, Avengers based in Stark Towers, etc.) Don't follow Ultimates 3, cause I think even fans of the ultimates can all agree that it SUCKED.
Just because it's the Ultimates story doesn't mean they have to use every detail. Just delete the Black Widow kills Hawkeye's family subplot and keep her a good guy, lose all the giant man beats wasp shenanigans, the defenders, Hulk trial, all that. Just have Giant man upset that he spends more time in the lab than in the field, he gets in a fight with jan (not physical, just a common verbal fight like couples get in), but he has a chance to redeem himself when he is the one swatting UFOs out of the air like flies.
The Ultimates is too tailor made for the cinema to completely ignore. You just have to ADAPT it, like any other comic book movie. I'm sure other avengers stories will influence the movie too.
And the point about people wanting their comic movies to be more fantasy than reality? Let's see...someone help me out here...what was that one movie that came out a little while back about the bat dude and the guy with the face paint? Over rated or not, ask people what they liked the most about it, and other than Heath's awesome Joker, they'll say "I like that it was
real" (even if real isn't neccessarily the best word for it). Obviously, with Thor and a giant green monster, that level of
plausibility (I like that word) may not be as reachable, but if the Ultimates was able to get it down to a level where people were calling it "realistic", you can bet that it's something that the writers/director/actors/crew/whoever will be looking at in the making of this film, as RDJ has already mentioned that trying to cement all these characers together in a "realistic" way was something they were looking at and were concerned about getting right.
That's my 2 cents anyway.

t:
PS
I DO hope they use the scene when Hawkeye is captured and escapes. That is the epitome of awesome. Maybe not fingernails (which would be a little grusome for the kids), but loose screws or something. He takes out one guy, the guy falls on his lap, uses stuff from him, etc.