Giving the guy the benefit of the doubt, but his Ultimate FF wasn't dark. It was basically Harry Potter meets Fantastic Four with the Baxter Building as Hogwarts and Reed Richards as a scientific Harry Potter. That would probably fit well with the whole "How do I get more of that sweet sweet Twilight money after the franchise is over?"
An FF with a young cast of 20-somethings would be exactly what the movie franchise needs.
Reed was effectively an indentured servant of the Baxter Building, poached at a young age to build them super-weapons. He was also portrayed as a troubled young man with an abusive father, incapable of relating to most human beings while desperate for recognition. He was also wracked with guilt over Ben's transformation, worse because while the original story had Ben know the risks of going into space on an experimental craft, Ultimate Ben just stopped by to see Reed on a college road trip only to get turned into a giant rock monster by being in the same general area. There were a few saving graces in his life, most notably Sue, but it's pretty easy to see how he went bad once those lifelines were gone.
Also (as Omar Karindu once pointed out), the Ultimate Fantastic Four never really discovered anything beneficial for humanity. If anything, they just found trouble that caused civilian casualties (for example, the Zombieverse) . And the secret civilizations they found were far more corrupt; for example, while the original Namor was a tragic anti-hero, Ultimate Namor is just a murderer and a rapist.
This isn't an indictment of Ultimate Fantastic Four's quality, just commentary that everything had a much harder edge.