Magneto has more charisma, magnetism even (you know I had to!).
Doom on the other hand has ruthlessness and drive beyond Magneto's capacity. he has a thirst for absolute power which Magneto's rarely, if ever, demonstrated.
as a leader in a tight spot, Doom is the better. his survival instinct, his assessment of a situation - especially a fluid and abnormal one - is far better than Magnetos, in fact far better than any 'mortal' in Marvel imo.
as a leader to look after a state, to keep the people in line without recourse to brutal measures, Magneto would be better. though his capacity for sentiment is actually his greatest weakness, imo. I'd still rather see a flawed and humane "man" in charge, than what is essentially a calculating and inhumane machine driven by the need for power (security? safety?) and his own vanity.
don't get me wrong, if Doom and Magneto were leading two warring nations, I'd much rather hold shares in the stock exchanges of Doom's nation than Magneto's for I can be quite certain that Magneto and his nation were "doomed" but, I'd most certainly not want to be a citizen in Doom's nation... the fact that at any moment I could be sacrificed as part of a gambit or a battle in order to win the war ... that's very much the way of Doom.