My view is the Skrulls. Establish the connection between the Fantastic Four and space. If they want to continue with a slightly darker tone,* there can be a bit of a paranoid alien conspiracy aspect since you're dealing with shapeshifters. Finally, you can add Super Skrull as the threat at the end.
* Although to make it really dark, keep the original solution of brainwashing some Skrulls into thinking they're cows for the rest of their life.
The only problem is this: One thing the Skrulls did was impersonate the Fantastic Four in order for the public to hate them. I'm not convinced the first movie will make them appropriately liked enough for that to work. Maybe save the Skrulls until after that's been established.