In issue 170 or so of the X-men Doom has them captured and Storm is being treated to his mannor, he tells Storm "I have forgotten more about war than you will ever know." Stark is intelligent as an entrapauner but Doom is hungry. He has the value to discard things of importance once he is through with them. I think Doom could take down Stark. He's smart enough to listen.
Iron man is in no way on the same level as Doctor Doom....come one...more firepower?....Doom has had armor that has made him a cosmic being, possessing the power of the Silver Surfer, Galactus!!!, and yes, even the Beyonder...Iron man isnt even the best Avenger...He's a good business man but not nearly as intelligent or deadly as Doom.
Dr. Doom is willing to kill, while Iron Man is not. He is one of the most powerful beings in the universe, and Iron Man would most propably be taken down with ease. Plus, Dr. Doom looks cooler. He doesn't need a lot of different weapons to win, Doom just has his strenght and his skill. Iron-Man would not stand a chance.