Reed was imprinted with Doom’s entitlement and ruthlessness (as evidenced by how callously he dispatched the Frightful Four), while Doom gained Reed’s more noble qualities (best shown when he voluntarily goes to the Marvel Zombieverse to save the world).
It makes slightly more sense this way, as we were already shown a possible future for the Four - with Sue going off the deep-end after Johnny’s death, shacking up with Namor, giving birth to (and indoctrinating) Franklin, and Reed becoming a freedom fighter in the N-Zone - and Reed was still his heroic self.
Victor’s contamination of Reed’s mind lingered until “Ultimatum" and he couldn’t rely on his friendships anymore.