Travel site aggregators face challenges when compared to airlines that market directly

If you are a budget-conscious traveler, there is a chance you've used a travel site aggregator like Orbitz to book your air transportation. Or, perhaps you shopped around on multiple aggregators, and made your final booking on an airline website. Did you ever wonder if you were presented with all airline options, or what kind of itineraries you could have received had you explored all airline sites one by one? Between aggregators and airlines, who ultimately has the upper hand?