An odd issue by What If creator Roy Thomas, but I think it's because he's still testing the format. I've always believed the series was better with actual turning points, stuff that you could imagine the Marvel Universe's Sam Beckett leaping into to set right again, than in trying to rewrite Stan Lee's brain somehow.
Because that's what What If? #6 is. Like Thomas' Hulk story in #2, it second-guesses the original premise rather than find a logical reason why the story should take that turn. I don't know where the idea the FF's powers are based on their personalities (see The true history) originated - it might be this very comic - but I like it, and it's a good template for all Marvel Universe mutates. Bruce Banner had a hidden frustration, Peter Parker felt like a creepy, Matt Murdock saw beyond the limits of his poor upbringing, etc. As for the FF, see below...
What If Vol.1 #6 (December 1977)
Based on: Fantastic Four #1
The true history: The four astronauts get a mutating dose of cosmic rays, the effaced Sue Storm became the Invisible Woman, and her hot-headed Johnny became the Human Torch. Ready to go to any lengths for science, Reed Richards got the power to stretch his body. And Ben Grimm's hard, brutish demeanor awarded him the rocky skin of the Thing.
Turning point: What if different characteristics of the Fantastic Four informed their mutations?
Story type: From the bottom up.
Watcher's mood: Xavier with a migraine.
Altered history: Ben, who's always loved to fly, grows dragon wings and calls himself Dragonfly. Sue's pliable personality gives her Reed's old powers, and she is Ultra-Woman. Johnny's love of cars translates into his becoming a living robot who controls machines... Mandroid! And Reed, being one of history's greatest minds, turns into Big Brain - literally just a flying brain with various mental powers. Not quite as iconic.
They still show up on Doctor Doom's radar, however, and Doom makes Reed an offer: To make him a body. But Big Brain already has a body, the Baxter Building itself.
But Doom still manages to kidnap the brain to turn it into the computer he needs to run his time machine. The FF follow, and they fight him in varied - and frankly, gross - ways.
In the end, Big Brain zaps Doom, which somehow transplants his consciousness in Doom's body.
And did Sue and Reed still end up together despite his new, mutilated face? The Watcher may be a voyeur, but he can keep a secret. Look, the Reed in this timeline's pretty ugly, but she's no catch either.
You see what I'm sayin'?
Books canceled as a result: None. Though I'm not giving this iteration of the FF long to live. The leader looks like a villain in a powder blue skirt. Johnny's powers are highly stupid (cosmic rays somehow turned him into gears and circuits). The female protagonist has the grotesque powers. Dragonfly is a lot less interesting the Thing. And oh, they took out their greatest archenemy in the fourth issue.
These things happen: No. No they do not. Though the FF's powers have sometimes evolved or temporarily been tweaked (as with every superhero published for a good length of time), the Four have pretty consistently had their original abilities for almost 50 years now. For a story in which a Reed Richard stand-in deteriorates into a flying brain and then even less, see Adventures of Superman #466, a homage to the Fantastic Four that nonetheless spawned an important character for the DC Universe. That Reed became the Cyborg-Superman! It's all in that issue, which could be called What if the Fantastic Four's dose of cosmic rays was lethal?
What If? #6 is a failure. Not just because it doesn't obey the rules of the series, and not just because Roy Thomas chooses some pretty lame powers for the heroes, but because it spends all of its time on a single big fight, and scarcely enough on the consequences of his changes. Next time, the series tries something else with its format.