I don't think it's all that incongruous. The thing that makes Doom both awesome and a recurring villain is his pride. His pride allows him to be the terror of the world that he is, because he WILL NOT ALLOW HIMSELF to be beaten. Defeated, yes, but not beaten. All defeats are mere setbacks - Doom knows that he will achieve his goals in time, because he is DOOM, and therefore destined to rule. This allows him to spring back again and again and again, becoming more and more formidable as the years go by. On the other hand, his pride is the very thing that allows him to be defeated repeatedly in battle. Doom is convinced that he is superior to any adversary, and therefore gets taken by surprise on a regular basis by the fact that his adversaries generally have a thing or two up their sleeves themselves. When you KNOW that such and such renders you invincible, simply because YOU have put it in motion, you tend to ignore the fact that you have the same human frailties as anyone else - it's by taking advantage of these ignored frailties that his enemies tend to beat him. This blindness to his weaknesses is also the reason why Reed Richards is the perfect enemy for him - he's the one man on Earth who rivals Doom for sheer mental acuity. On a certain level, Doom knows this, and it drives him crazy - NO ONE RIVALS DOOM! And BECAUSE no one rivals Doom, Richards MUST be inferior in some way, and Doom's mammoth ego demands that he prove this once and for all by eliminating him and his team. It is this obsessiveness that makes Doom the great villain he is - and arguably, he never would have become that without Reed's presence in his life. So him being the FF's archvillain makes perfect sense to me.