Well, I think in some regards a way to "darken" the tone if that's what they really want to do, all they really need to do is set part of the movie in Latveria, with a PROPER DOOM. That would darken the tone quite a bit right there. You don't need to have say, Sue get assraped by Doom and get preggers with his demon spawn. But you have Doom planning something really really nasty. Don't need to give the origin story again, you can do that in the opening credits sequence ala Spider-Man and the Hulk. We all know the story, let's just move on. Start out light and breezy, then Doom comes into the story with reports of him sending Doom-Bots and troopers into neighboring countries like say, Symkaria (could even have a brief Silver Sable cameo) and other Eastern European countries. Maybe then the tone shifts to a more dark and serious one, Reed is maybe called before some military types and questioned at end about Doom and what his motivations and weaknesses could be and how they can stop him. This time Reed is DR REED RICHARDS - SUPER GENIUS from the comics - the one that every brainiac in the MU wants to be. And y'know what he can be at least 10-15 years older than whoever plays Sue. Although a bit older Sue wouldn't be bad. I always did like the Jim Lee FF era Sue, where she's a pretty savvy businesswoman, not really a science geekette but she's not only well versed in fashion. She's not Janet VanDyne - honestly I think had they cast Ioan and Jessica as Hank Pym and Janet VanDyne (Ant/Giant-Man and the Wasp for those of you who aren't up on your Marvel Knowledge) that would work just great. But not for Reed and Sue. Anyway... Sue could be working the Fantastic Four Inc's contractors and working on getting Reed the gear he needs. Johnny and Ben would be the comic relief as they have been for the past 40 years and honestly they would be the ONLY TWO of the original Four I would keep. I didn't mind the black Alicia, she was far spicier than the 'original' and eh, so what. She's black, he's orange rock with a white guy inside. Big whoop. Chris Evans is exactly like Johnny. In his younger days I would have cast Brad Pitt, but he's too old now. Doom can really be anyone in the suit and mask, just need a good voice, and even that can be digitally altered so y'know what, as long as the fraggin DIALOGUE is good, and well acted. Heck get Frank Welker or Peter Cullen, they're masters of that shit.
Maybe even bring in some of the super-natural aspects of Doom where the reason why he's taking over so much of Eastern Europe is so that he can create a large enough power base so that he can acquire enough supernatural elements to rescue his mother from Hell or something.
I mean, there's enough you can do to the next movie to make it "darker" than what we got so far, but still keep the lighter, family feel of the originals. Maybe even have Sue reveal that she's pregnant toward the end and Doom is ready to kill her, and he finds out she's having Reed's baby and as much as he would love to hurt Reed that way, he finds out that her son has a lot of power inside of him. Power that he may be able to use later. So he spares her life. And ends with him keeping an eye on them from their HQ or something. Kind of forshadowing Franklin's awesome reality warping power.
"Someday child... someday you will reshape reality. A planet for Doom!"