The homoeroticism aside (I know, I know, just bear with me) having Doom there, as Moon points out, would've been very, very poignant because Reed is in love with being a superhero, goes to an alternate world to see a better version of himself, a better world, but it turns out to be **** and the only good thing is a man who was once his best friend and now his sworn rival who tried to kill him. Reed would've gone from idealism, to pessimism, to idealism once more when Doom sacrifices himself. And if that wasn't enough, the scenes in the alternate universe would've been even MORE tense because Reed wouldn't have known how to handle Doom, and the Doom we see would've hated Reed regardless. So now you have two sworn enemies who've hated each other for years, been friends before that, but have never met, forced into a situation where their only hope for survival is to work together, each repulsing the other while at the same time, being the only symbol of hope for the other. I think it would've been damn good.
Plus - think about all the homoeroticism. THINK ABOUT IT.