Here are just a few random ideas,
It should start like the (Norton's) Hulk started, with the FF already a super team. This would not only present it as a semi sequel to the other films but also start the movie out the way the first FF comic started.
We would then see a flash back of their origin, but not the origin from the Alba film, or the 90s film.
This origin would be more like the comic, only instead of trying to reach space first.
Reed Richards is trying to reach Mars first.
(In the comic Ben mentions the dangers of Cosmic Rays because no one had been into space yet.)
In this film the Dangers of Cosmic Rays are a threat because no one has been to Mars yet and no one knows what dangers await.
Not sure on who the villain would be, since Doom was never done right in the movies but would now be over kill and hogging to spot from another FF villain. But Doom needs to be done right eventually. (Rebooting Doom is a Post all itself.) Maybe have the FF face off against the Mole Man and a giant monster. Start them off with something a little fun maybe.
Also, in one of this film's sequels perhaps, introduce the Negative Zone.
Oh, I know. Perhaps have the enemy in the first Reboot film be the Skrulls from Outer Space. Maybe even use the comic's idea of having the Skrulls try to discredit the already famous super team by masquerading as them. (Again, sort of alluding to the idea that there were other films setting up that they are famous, but also not being a sequel.)
I am also not sure about their costumes, don't want the spandex from the original movie or the last two. Maybe start out using the originals as a jumping off point. Make them not so skin tight, and make the 4 symbol larger. Maybe make the blue a little brighter, not bright blue like the original 90s film had it, just not a real dark and muted blue like the last two had it.
(Also I would have maybe half of the movie, OK maybe just half of the first half of the movie, showing them fighting without costumes. They didn't get costumes until issue three. But this idea I can take or leave. The movie could start out with them already having costumes, and already having a base and being famous. Plus the Skrulls introduce the idea that anything can happen in the FF films.)
Also, in the original comics Thing didn't have a distinctive look at first, and Doom's costume wasn't like it is now. They both looked different initially. So it might be reasonable to use that when altering their looks. Maybe Ben's body changed over time from a rocky mud ball looking monster to a solid rocky monster.
And Doom's armor could become more regal when he takes over Latvaria.
(But again, its not really a sequel)
The theme of the films should be Family, and the movies should be somewhat family friendly. Like the Incredibles movie was.
Reed should also invent some unreal, fun, and wacky, inventions. Make them more Space Adventurers, that tackle anything. Anything from fighting the Silver Surfer and Galactus, to Dr. Doom, to the Skrulls from Outer Space, to pirates in the past, to Atlantians under the sea.
Anything should be able to happen in these films.
Oh, one last thing. Maybe have references to other Marvel heroes too. Like Johnny Storm can be reading a Hulk comic, or Sue can be reading about Spider-Man or maybe just reading the Daily Bugle. Or maybe Reed mentions a lawyer by the name of Matt Murdock. Or Reed gets a phone call from Tony Stark, or the FF are met by SHEILD agents after saving the day. (Not just big moments at the end of the film either. Sprinkled into the film.)
Just a few random ideas on how to reboot the ff film franchise.