^^ This. She always seemed to answer directly to Picard, not Crusher, and I always got the sense that Troi's role on the Enterprise was Picard's prerogative, and probably a unique position. While Troi was the ship's councilor, Troi was also an adviser to Picard, particularly in cases of diplomacy, and basically filled a dual role. Due to her empathic abilities, she was supposed to help Picard determine the truthfulness or emotional state of mind of the other side, etc. While other ships and starbases certainly had ships councilors, Troi being so high up in the command structure of the Enterprise is very unusual, and possibly unique.
Both Troi and Crusher were commanders, outside each others' chains of command, and thus were equals. In fact, both technically were in positions where they could relieve Picard of command, if warranted, due to medical reasons.