Fantastic Four/WMG

Franklin's powers
Regardless if his Parents were altered by cosmic rays before he was conceived Franklin would still be a mutant. Made evident in House of M where he was a Mutant patient of Emma Frost and apparently conceived before Reed and Sue travelled into space.
 * However, having "Mutate" parents possibly enhanced his abilities to reality warping levels.

Odin was the one who really destroyed Galactus.
this is a WMG for Rise of the Silver Surfer. Lets face it the Silver Surfer really didnt have the required energy or strength to take down a FRIGGIN SWIRLING BALL OF DOOM that could destroy planets by almost just thinking it.

To boot it was Galactus his/itself that gave the Surfer his Power Cosmic in the 1st place, also its doubtful that Galactus would really give him enough cosmic energy that the Surfer could possibly use against him. So the only logical conclusion is that Anthony Hopkins Odin from the Thor film is the one being powerful enough to take out a omnipowerful creature like Galactus pretty easily.

As it states in the Thor WMG the Asguardians are clearly on a technical and power base at par with Time Lords also the film itself stated that for unknown eons Asguard protected Earth and countless other planets for so long they were worshipped as gods by some species (including humans). So Odin probably saw Galactus attacking Earth and the Surfers heroic sacrifice so he used a Cosmic Tesseract Cube to blow Galactus's gas based ass into oblivion.

However the Fantastic Four or noone else on earth saw this so everyone simply assumed it was the Surfer.

The Fantastic Four are actually anarchists
Look at their logo in the movie - it almost looks like the circled A, doesn't it? Hence, Doctor Doom may be a Strawman Political standing for every authoritarian (read: non-anarchist) government.

Dr. Doom is the most arrogant man in the world...
...but if there was a chart Reed Richards would take the number 2 spot.
 * Doom is definately the most arrogant man in the world, that's not guessing, that's fact. As for number 2, I guessing Tony Stark just beats Reed.

The Fantastic Four got their powers on an attempted moon flight in 1961.
They're still roughly the same age in the present day because they routinely time travel. They'll spend a few days on an adventure, then jump ahead a week or two.

Doom's machine to contact his mother...

 * Didn't work. His calculations really were flawed and it blew up in his face.
 * Didn't work. His calculations were correct but it's impossible to contact the "nether world" because it either doesn't exist or is totally beyond the reach of technology.
 * Didn't work. Doom was right to mistrust Richards, who sabotaged it for fear of the damage it would do if it were fully activated.
 * Worked. It exploded because it was channeling hellfire.
 * Worked. But it didn't have the right shielding.
 * Worked. Doom's face was scarred when a being from the other side (possibly Mephisto) touched his face and "marked" him as evil.
 * Worked. His face wasn't scarred, but he saw what was being done to his mother, went insane and destroyed the machine.

Film Galactus was actually Ego the Living Planet in disguise
A giant power hungry planetary dust-cloud that eats other planets fits Ego more than it does Galactus. Silver Surfer might still have gotten his powers and served the real Galactus, but at some point he ran afoul of Ego, who brainwashed him into finding worlds that Ego could feed on while masquerading as the surfer's true master. It also explains how easily Silver Surfer was able to defeat the dust cloud because it wasn't the true Galactus. In order to beat Galactus you need something on the same power level, while with Ego you need only destroy him as you would a planet.

It's always a Doombot
Victor von Doom has been dead for years and every time the Fantastic Four or any other hero meet Doom, it's a Doombot. It's already canon that the Doombots are programmed to believe they are the real Dr Doom, and are so well-made it's practically impossible to tell they are robots. So, the human Doom is dead and "Dr Doom" is just a bunch of Doombots running around, each one thinking it's the real one.