The MCU Fantastic Four

Optimus Prime said

Not doing the big bad is a bold move

it can be done (Batman Begins not using Joker) but it’s a risk

i wasnt a huge FF fan but wasn’t Doom with them on the shuttle?

it would be doubly odd not to use him if that’s the case

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No, Doom was not on the shuttle with them. That was in the insufferable first crack at a film version. Doom's origin had basically nothing to do with the FF's origin. He and Reed knew each other, but that was the only "tie" between them.