As for the source of their powers, I'm surprised that so many commenters here would expect them to use the old cosmic-ray origin. Previous Marvel movies have updated the characters' origins -- Hulk was created by a supersoldier formula (or nanotech in the Ang Lee version), Spidey was created by genetically engineered spiders rather than irradiated ones, etc. The previous FF movies replaced the "cosmic rays" with some sort of exotic space storm. I'm sure the new version will find its own way of updating the technobabble.
IIRC, the Ultimate version of the Fantastic Four (and Dr. Doom) got their powers from a teleportation accident that had them briefly exposed to another dimension. It's very complicated.
Right, a useful way to get around the cosmic ray problem, and it makes me wonder if FOX will make an Ultimate version of the FF similar to the recent Spider-Man movie.
And, regarding Ben's cure, it seems that the real simple explanation would be that the cure could work but something disastrous has to happen. Like a life has to be traded for a life or something; or it was only Doom's physiology that made the machine work in the first place.