One thing that I've always had issue with is Doom. I've heard he's supposedly the biggest bad of all the bads in the primary Marvel universe, but what are his powers? What makes him so powerful? How come I can't think of a single big-time Marvel event (granted, I don't know a ton) where he even participates?
I've seen the 2005 movie and the sequel and his powers are electricity? Manipulation of some kind? Being evil? It's like he's a male Scarlet Witch - his powers are just whatever the plot demands. And I've heard the same sort of power ambiguity exists in the new movie.
That's the funny thing about Doom; in the comics he doesn't really have any powers. Doom is a super genius like Reed, and Doom's armor is essentially an Iron Man suit. In fact, one of the more memorable Marvel stories is when Iron Man and Doom tangle over a time machine and end up in the time of King Arthur; the only way they get back home is by sharing armor components to build a new machine.
So Fox had an Iron Man type character in their movies before Marvel did, but they ignored that aspect of the Doom character.
What they were doing in the Tim Story movies was focusing on the natural elements. The Fantastic Four represent the four elements (earth, fire, wind and water), and they were trying to make Doom into the fifth element. In some cultures iron has been considered the fifth element; in some cultures electricity is the fifth element; the Story movies just threw it all in to see if it would stick.
As for Doom being a major threat, it comes from two areas. Doom is the King of his own country; he's like Saddam Hussein with the skill to build a particle accelerator from scratch. He has a full army behind him of both real people and robots he created. The FF even went in one time and freed the people of Doom's country; the people responded by fighting the FF to get Doom back. Doom is actually good to his people and in terms of medieval times he would probably be considered a good king; he just wants to control everything.
The second area that makes Doom a major threat is his iron will. The biggest Marvel U event he was a part of was Secret Wars (both the old and new series). In that story, a god-like being called the Beyonder set up a Star Trek style battle royale between good and evil to see which was superior. While the heroes and villains just play their parts in business as usual, Doom doesn't participate. Instead he works toward taking down the Beyonder himself; and even though the Beyonder strips Doom down to nothing but blood and bone, he still never gives up. Doom gets in the Beyonder's head and turns his own power against him; then Doom takes the power and essentially becomes a god. Ultimately Doom is beaten by the heroes using a similar tactic, but they do it as an army against him; Doom did it alone.
I think Fox's best bet is to absorb them into X-Men somehow.
There is a built in way to do it, but it would take skipping ahead in the FF time line. Franklin Richards (the son of Reed and Sue) is a mutant who has the power to bend reality (i.e. creating a second earth on the other side of the sun); and this has caused the X-men and FF to tussle a few times. Franklin is dangerous because he's just a little kid and doesn't know how to control it; Xavier wants to take Franklin away to teach him but Reed and Sue think they can handle it and don't want to give up their kid.
Franklin also had ties to a four person kid team called Power Pack who were usually tied into the X-men universe even tough they weren't mutants. I don't know if Fox has the rights to them, though.
