You might want to also consider his career overlaped with Valverde's and, in the classics department, the latter was much more the specialist, in an age when, following Armstrong's trajectory, specialization had really peaked. That and after Contador's career blip, to win grand tours he had to deal with the new force in town, a.k.a Sky and Froome. Ixnay any lingering classics ambitions. Plus he was Spanish and, bar Valverde, the Spaniards have never really excelled in the monuments, being much more stage racers as Indurian epitomized. Even the Italians have been historically more a force in the spirng classics campaign than their Iberian cousins. Nibali benefited from this; that is from how community, tradition and heritage makes one feel what it means to be a cyclist.Contador was never gonna be a prolific one day winner cause he lacked the sprint and wouldn't really destroy everyone at <5 minute climbs. Also at the peak of his powers Il Lombardia was much more of a puncheur race.
Frankly, there's a big, sad void of one day races that are suited to pure climbers, and I would love if there were a few biggish ones as an alternative to Vuelta for the climbers.
At any rate, at his peak (when his TT was among the best in the world), I say Contador, with an adapated approach/mentality and without other hickups or distractions could have won MSR, LBL, San Sebastian and Lombardia. Of course, it would have helped to have been Italian. But we can't change history.