Just because an archenemy exists, does not mean that its important. Doctor Doom being the archenemy to The Fantastic Four stems primarily from over usage and the retreading of the Reed/Victor relationship much like Batman and Joker. Archenemies don't exist because they are just that important of a villain (you don't gain importance just by existing), they are archenemies because they show up enough or are used in such a way that every time they confront the hero(s) the stakes are high to them. Good writing is always important but that kind of villain exists either due to a lack of villains or the refusal to use others which as seen in FF they tend to use Doctor Doom a lot.
Doctor Doom pretty much only occupies the position he does due to the inability or refusal to use anybody else. Good stories do still happen but Infamous Iron man was necessary due to the long history of Doom coming in an upstaging what's going on in Fantastic Four. Fantastic Four is not about Doctor Doom. A major difference between Green Goblin, Joker, or even Lex Luthor, is that Doom is here far more consistently and therefore occupies a spot in the book never-mind that FF is again, not about him. Suffice to say he really shouldn't be here nor even so quickly back as ruler of Latveria.