What would I have done differently? Everything.
First, make Doom the ruler of Latveria. As the king, he'd be called King Victor but his family name would be Von Doom and he would refer to himself as Doctor Doom by the end.
The setup revolves around the mysterious Eastern European country of Latveria. Having declared independence from the Soviet Union, it entered into a long and bloody civil war. Young Victor, himself descended from Latverian royalty, fled to the US during the Soviet era. Educated in American schools, Victor proved to be brilliant and went to college with another prodigy, Reed Richards but while Reed was interested in science for the purest of reasons, Victor harboured a desire to return to Latveria and take back what he believed was his. He does this during the civil war, leading what is effectively a peasant revolt against both the forces still loyal to Russia and those supported by the west, in what is the last proxy war within the Cold War. Conquering both sides, Victor is declared undisputed ruler of Latveria, making himself an enemy of the east and the west.
Then Latveria goes quiet for years. Victor closes the borders and creates an electromagnetic dampening field around the entire country so that not even spy satellites can get a good picture of what's happening there. He creates what the US calls a European North Korea.
All of this is backstory for your sake that may be referenced but is secondary to the plot. All you really need to know is that Victor is ruler of Latveria and the world sees him as a tyrant.
Years later, the Fantastic Four have already had their outer space mission and have gotten their amazing powers and are active as heroes in New York. When an American spy drone is shot down over Latveria, it is the first contact between Latveria and the outside world in over a decade. The administration decides to send a small, covert team across the border, into Latveria to see what's going on since all technological efforts to spy on the country have failed. However the team is captured and for the first time since closing the borders, King Victor addresses the world, accusing the US of sending assassins to kill him and threatening untold destruction on the US and the world.
Hoping to defuse the situation, since the world has no idea what kind of weapons Victor has at his command, they propose to send a negotiating team via the UN to Latveria to work out a lasting peace. They are surprised when Victor agrees, however he insists that Reed Richards lead the team as they knew each other at college and Victor respects his intelligence. He also invites the rest of the team to join Reed and see the kind of country he has created for themselves.
The Fantastic Four travel to Latveria and are amazed to find that instead of a poverty stricken and oppressed country, Latveria is a social and technological marvel with every need of every citizen taken care of. Victor explains that every citizen is free to leave but most choose to stay, the only requirement being that they swear fealty to their king. Reed in particular is amazed by this apparent utopia Victor has created but is still concerned that it's a dictatorship and urges Victor to open up the borders and let the world see and share in his advancements.
Victor agrees to leave Latveria and travel to New York to address the UN, in the hope of creating a lasting peace. He invites the Fantastic Four to stay at his castle and enjoy his hospitality while he makes the arrangements for the trip. Of course, it turns out to be a trap. Victor has designed special cells for each of the Four, meant to nullify their powers, including Ben's who finds that Doom has returned him to his human form.
Victor reveals that the only reason he agreed to the peace negotiations was to get the Fantastic Four out of New York. He tells Reed he will share his advancements with the world and make it a better place but that since the world will only see him as a villain, he will have to force the world to change and if that means embracing the role of villain, so be it. He remembers back in college, when people would make fun of his name, Von Doom, calling him Doctor Doom. Victor decides to embrace that and leaves the Four in their special prisons to travel to New York.
Once Doom is gone, Reed immediately gets to work on figuring out how to escape their cells and thanks to some scientific mumbo jumbo and convincing Ben to return to his rock form, they do. However, they can't call the Fantasticar to pick them up because all outside technology is disabled by the dampening field, so the Four have to make their way across Latveria to the border, hoping they can get back to New York before it's too late. The people of Latveria, unwaveringly loyal to Doom, make every effort to stop the Four from escaping the country.
In New York, the skies above the UN building darken. The world does not yet know of Dooms intentions but they are soon made clear as he arrives at the UN, not in a limo, not in a helicopter, but in a massive, flying warship. Speaking from his throne on the bridge, Doom declares that the world needs a single, strong ruler to unite them, not petty, squabbling politicians and proceeds to fire the warship's main cannon at the UN, completely destroying it and killing all the delegates inside.
The response is immediate as military jets scramble and forces pour into Manhattan. Doom is prepared for this assault however and massive battle takes place, with the warships guns targeting the jets and countless Doombots being unleashed against the soldiers on the ground. The military finds itself completely outmatched and after an epic, losing battle, they are forced to retreat and concede temporary control of Manhattan to Doom. They attempt to evacuate the island but Doom refuses to let them, holding Manhattan hostage and giving the world 12 hours to surrender.
Meanwhile, the Fantastic Four fight their way through Latverian military units, comprised of both people and bots and finally make it to the border, where the Fantasticar is waiting. They learn what is happening in New York and immediately rush there to help.
They arrive with time running out and lead a campaign against Dooms forces, hoping to disable the warship and force Doom to surrender. After a long battle, the Four reach Doom and have their climactic showdown. Doom is finally beaten but not to the point of surrender. As his warship crashes into the sea (with Sue using a forcefield to prevent it creating a massive tidal wave), Doom escapes and retreats back to Latveria. The day is saved, at least for now but Doom is still out there.
As cleanup in New York begins, Reed returns to his lab in the Baxter Building and discovers a strange energy signature heading towards Earth. Doom has also discovered the same signature and begins making new plans, unaware that the signature is that of the herald of the devourer of worlds, Galactus.
So yeah. That would have been my F4 movie, or at least one version, with Doom as ruler of Latveria, trying to take over the world. The origins of the F4 would have been told in a news broadcast when a reporter is talking about Reed agreeing to be a part of the negotiating team, as a bit of exposition rather than going through the origin from the start. Doom himself would be scarred and wear the mask and armour. Unlike the other films, he wouldn't share the same origins as the F4. His power would be purely technological, with the magic aspects being introduced in the sequel.