Well, I mean the problem is that there wasn't really any conflict in the movie so they just tacked on Doom in (literally) the last 20 minutes. The first 20 minutes is just Reed and Ben. Then they introduce Franklin and Sue. Then Johnny. Then they build it, go to the planet, and come back. There's no villain in the first half of the movie except just "progress" I guess. The planet is sorta evil and the main guy is sorta bureaucratic, but that's it.
Then the second half really is a different movie. Bureaucratic guy becomes "take over the world" evil, Reed runs off, Ben gets mad that he was abandoned, Johnny embraces his powers, and Sue is just helping or whatever. Then Reed comes, fixes the machine in ten minutes, they get Doom back, he tries to destroy the world, and they team up to beat him.
So there's no villain until Doom shows up the last 10 minutes. Doom wasn't really a bad guy before he transformed. He never endangers the other guys (except maybe convincing them to go in the first place). Bureaucracy guy just wants to move the project along - and even when he's using Ben (and then Johnny) as weapons, both seem pretty okay with it. Doom is just tacked on so there's someone for them to fight.
If it was me, I'd leave the first part of the movie almost exactly the same. I'd have Doom refuse to come back but start working on his own gateway with the Latverian government. Reed and co finish the gateway first, go to the planet, and they get their powers by some accident. A year passes. Reed doesn't run off because that plot doesn't go anywhere. The government uses Ben on some missions, but Franklin's been able to keep Johnny on the sidelines while Reed and Sue work on the gateway. Meanwhile, Doom finds out that Reed got it to work when he sees what's happened to Ben. So Latverian soldiers attack the facility, and the Four are able to fight off soldiers using their powers (an action piece where they work individually because it's super powers vs. normal soldiers). In the chaos, Doom sneaks in and steals a vital piece to the gateway and gets away. Back in Latveria, he completes his machine and goes along with a couple soldiers to Planet Zero. Something bad happens, Doom gets left behind, one soldier dies, and the last soldier comes back horribly mutated (I don't know any other FF villains but Doom and Galactus so let's just say it's either one of their villains with a new origin or it's a new villain entirely). The mutant starts wrecking the lab and Latveria asks for the Four's help. So they go, struggle at first, and the defeat him as a team. End credits scene shows Doom on Planet Zero, using his powers to create a gateway on his side.
More action, no cramming Doom into the finale, an extra action piece. Not changing a ton. Could've worked.
I do wonder how Trank figured on ending the film. Because, again, there's no villain in the part of the story he seems to be affiliated with.