Set it in the 1960s, but make it only set in the 1960s. It'd be our window to the '60s MCU.
No origin story. It's 1961 and the Fantastic Four is an established group of celebrities, with Reed known to the world as a genius millionaire scientist (and a top developer at NASA).
They are known to SHIELD (Director Peggy Carter), of course, as a team of super-powered individuals. They can pay lip service to their origin, referencing the Mole Man and Doctor Doom. Over the course of a 13-episode Netflix series, they meet the Watcher (Stan Lee), a cosmic entity who has become infatuated with Earth, but warns them of an impending invasion by the Skrulls.
But it's not the Skrulls they should be concerned about. While they dispatch the scout ship and the Super-Skrull in a couple of episodes, the weather begins to become erratic. Hurricanes, tornadoes, the craziest weather patterns ever recorded hit Earth and specifically the East Coast. Reed uncovers Skrullish transmissions, and the UN building is visited by the Silver Surfer, the Herald of Galactus. SHIELD keeps it under wraps, but the meeting tells you that Galactus is a force of nature, light-years in diameter, that has consumed planets, and will likely consume Earth.
The Surfer is held in isolation and "interrogated" in every way imaginable, fruitlessly. He eventually aids the Fantastic Four into developing super-science that could disrupt Galactus and perhaps disperse it away from Earth. They also attack more Skrull scouts and other baddies who are taking advantage of the constant blackouts and craziness over the winter of 1961/1962.
In the end, the Watcher breaks his oath, and provides Reed Richards with a cosmic nullifier that imbues him with the ability to "persuade" the Galactus entity into leaving the solar system. The Watcher and the Surfer end there role in the series playing chess in Central Park, both finding themselves exiled to Earth.
SHIELD was caught off-guard by the alien invasions and ill-prepared for any of it or the Galactus entity. Director Carter resigns and forms the World Security Council to oversee SHIELD and all metahuman activity present on Earth. Reed gives her the nullifier, which is locked away in a vault deep within the deepest of SHIELD's archives. Where it promptly appears to blink out of existence.
Thousands of miles away, in Latveria, Doctor Doom is mulling over the events of the winter blackout and his own top-secret reports on transmissions revealing the Galactus entity. When he is visited by a mysterious man in a business suit, who provides him with the nullifier in exchange for taking out the Fantastic Four and SHIELD. The man's name: "Call me Kang."
Cast:
Reed Richards (13 episodes)
Sue Storm (13 episodes)
Johnny Storm (13 episodes)
Ben Grimm (13 episodes)
Alicia Masters (most episodes)
Uatu the Watcher (a few episodes) - Stan Lee (maybe CGI his classic form once or twice), might also reprise his role as Willie Lumpkin
Peggy Carter (a few episodes) - Hayley Atwell
The Silver Surfer (a few episodes)
The Super-Skrull (a couple episodes)
Howard Stark (1 or 2 episodes) - Dominic Cooper
Hank Pym (1 or 2 episodes) - a new actor playing younger Michael Douglas
Doctor Doom (1 episode)
Kang the Conqueror (1 episode)
The ultimate fate of the Fantastic Four is not delved into during this Netflix season. A potential 2nd Season (focusing on Doom and Kang) could allude to some things, and perhaps the Four could, in fact, disappear into the Microverse or outer space or another dimension or whatever, only to come back in modern times.
Basically, the idea is that this group of "extraordinary people" operating outside of traditional oversight is what inspired Nick Fury into developing the Avengers project decades later.
I'm still not sure about Namor. Atlantis seems like such a big stretch for the MCU, unless they can tie it into Attilan, which would be Inhuman-stuff which doesn't seem popular atm. Aquaman might force Marvel into developing Namor at some point. Perhaps he's better fit as a 1930s character, Marvel's First ...whatever..., from a long-lost society of powered people. That live under the sea. Somehow.