Okay, this is how I would have the Avengers work if I was in control of the Marvel Universe, this is how I would have the Avengers work with things like Civil War, WWH, Secret Invasion, and so forth.
First off, I would have the Avengers sent up into three teams - Mighty, New, and Dark Avengers. The reason for this is because the Avengers teams have became so large that you can't have every hero on one team.
The Mighty Avengers
This team would be like the "Old School Avengers" the kinda of team that would protect the whole world and fight villians like Dr. Doom, Ultron, and the Masters of Evil, this team would be like the main Avengers team.
1. Captain America (Rogers) - Leader
2. Iron Man
3. Ms. Marvel - Second in Command
8. The Wasp (Hank Pym)
This team would be like the "Street Avengers" this is the team that would fight villians that one hero can't beat by themselfs, but aren't to bad that you need ever hero on the planet to come and fight them, this team would fight people like The Hood and his gang or groups like the Sinister Six, and maybe fight a giant robot every now and then.
1. Ronin (Clint Barton) - Leader
2. Black Cat
3. Iron Fist
5. Luke Cage - Second in Command
This team is the "Black Opps Avengers" this's the team that will do the things that the normal Avengers can't, this team can brake the law if it means keeping the world safe, this is the team that has some of the most skilled Assassins, Spys, and Mercenaries from all over the world, this is the team where if the bad guy gose to far, he'll have a bullet in his head, this team dosen't mess around, this is also a secret team, the public doesn't know about this team's a ctivities. NOTE: I would also change the team members uniforms (Like Wolverine would wear his X-Force suit) to reflect the teams black opps feel.
1. Wolverine - Leader
2. Black Widow - Second in Command
4. Captain America (Barnes)
The Young Avengers will be much like they are now, but will work along side the New Avengers.
1. Patriot - Leader
2. Hawkeye - Second in Command
This team deals with other planets around the Universe, like helping stop wars between races (Skrull and Kree Wars) and help protect planets from beings that other wise would destory them (Galactus and Annihilus), this team will also make sure nothing like Secret Invasion ever happens again.
1. Nova - Leader
2. Captain Marvel (Noh-Varr)
5. Silver Surfer
With all of these team running around, there will be a group of the leaders from each Avengers team, this group will meet every now and then to make sure everything is going okay for each team, these meeting will have disscussions about wheater or not a member of one of the teams should be taking of f of the team or be switched out, teams will also disscuss whether they need some back up from one of the other teams (Like if the Galactic Avengers need help, the Mighty Avengers would send some or all of their team to help).
1. Captain America - (Mighty Avengers)
2. Clint Barton - (New Avengers)
3. Wolverine - (Dark Avengers)
4. Patriot - (Young Avengers)
5. Nova - (Galactic Avengers)
NOTE: The Avengers are not funded by the Government, the Avengers are funded by other groups such as Stark Industries and RAND Inc. and the Galactic Avengers have some connection with groups like Nova Crops and the Inhumans. Also, The team rosters will change over time.
5. Ant-Man (Eric O'Grandy)
6. Black Panther
11. U.S. Agent
12. Beta Ray Bill
13. War Machine
14. Blue Marvel
17. Union Jack
21. Sharon Carter
Now with all that's happened with things like Civil War, Secret Invasion and so on there needs to be some kind of group that needs to have the people's trust, this team will work with the United Nations about things in the Super-Human Community, like Damage (Civil War, World War Hulk), this team is kinda like the Illuminati.
1. Captain America - Super-Human Community
2. Thor - Asgard
3. Black Panther - Wakanda
4. Emma Frost - Mutant Community
5. Namor - Atlantis
6. Black Bolt - Inhumans
Now when it comes to the S.H.R.A. that would be like what happened in that "What If" Story where Captain America was told everyone's secret indenity, but a bit diffrent, where Both Captain America and Iron Man would know and work on making a way to train all of the heroes, and the Illuminati Avengers would play a part in this.
There will be two Avengers HQ, one on Earth in New York City and one in Space.
This base is not the same Avengers Tower, this is a whole new tower bulit off coast of New York City, to keep the public safe if the base is ever attacked, this base will also mostly be the base of the New Avengers.
Avengers Space Tower
This tower will orbit the Earth, keeping an eye on the whole planet as well as watching the other planets in the universe, this tower will be the base of the Mighty Avengers since they'll be dealing with threats all over the world.
Avengers Class: Quinjet