Adaptation is a tricky business any circumstances. Stories drawn from long-running serial medium will almost inevitably have periods of change, adjustment with the times, changes in creative teams, etc. Those changes lead to preferences, and nowhere are those preferences more divisive than in the world of comic book fandom.
For the record, I don't entirely understand why they've continued Fantastic Four past the initial run by Stan Lee and Jack Kirby. In fact, my perfect movie adaptation would take place in 1961 and not vary at all from the tone of the original comics... the only changes I'd want would be of addition, filling out the stories as they exist.
That's probably not big hit material and had they come to me to write or direct the movie, I would have worked to conceive a compromise. I think there has to be a way to update Doom, for example, without making him a wiener or a poor imitation of other supervillains, even less both of those things.
I think the key in there somewhere in starting with the core of what makes the character or concept work. Some characters this seems like it should be easy. I think Bryan Singer's The X-Men got the core concept of The X-Men, while his Superman Returns was shockingly off-target in capturing what makes Superman work (my experience chronicled in more detail here).
Batman, of course, creates no end of trouble with the vast differences between different versions and personalities over the years. Not only that, the different versions all have their own group of fans, many of whom, like the children in Legends of the Dark Knight, that their favorite/familiar version is the only correct one.
I thought overall Ghost Rider did a solid job of taking things from various periods in Ghost Rider history and blending them into something that could have been satisfying to fans of any or all of those periods... or would have if the movie itself had been more interesting in itself.
The Fantastic Four is possibly more complicated. There's the family issue. That's a big deal and they certainly shot for that.
I have to say that, in my opinion, the movie was missing the imagination of it. The boundless spirit of a group of scientific adventurers who could somehow stumble onto anything.
Mind you, this has not been true of every run of the comic either. I'm hardly the first to make the comparison, but here's where we must note that Lee and Kirby were very much the Lennon/McCartney of comics and new creative teams are stuck being something like guys trying to write songs for new Beatles albums. Usually it's considered safest to go with simple imitation, which, of course, misses a substantial part of the charms in itself.
But, man, that run, that spirit, is a comic book! And it could be a movie, if they'd at least try...
I want to make a side note here. One of the big selling points of Fantastic Four and Fantastic Four: Rise of the Silver Surfer seems to be the "family friendly" nature of them. All I know is that I have no specific interest, as a creative artist, in creating "family friendly" material, but my version, I would not have made Sue Storm get naked on the Brooklyn Bridge.
I don't know that I have any simple answers. I understand that there's huge amounts of money going into those movies. I also understand that there's tons of pressure from studios and fans not to make one of those movies, something that will embarrass everyone. I just think that too many of these movies are missing some spark of life, a spark that's there on the page, and I'd like to see it.