I think for the most part the Story films were pretty faithful. The biggest problem is the scripts were horrible, they used cheap CGI (Reed stretch dancing), and the stories were actually kind of boring.
One thing both the Story films and this reboot don't get is that we could care less about the origin, and the comics didn't either. Yes there's the story arc of Reed trying to cure Ben, and that was fine, but other than that, they spend most of the first film trying to cure their powers, and then in the end after a 2 min fight scene, decide they want to keep them.
As far as Doom, I still remain that Julian McMahon was a great choice. It's not his fault the writing was bad. He is great at playing characters you love to hate, and that's Doom in a nutshell. What's very sad is he said, how much he loved wearing the mask but in both movies they seemed to want him out of the mask for most of the movie.