Subacromial Bursitis or Rotator Cuff Tendinopathy: This condition is a common cause of deep shoulder pain, especially if it's intermittent and has been ongoing for years. The pain can be exacerbated by certain movements or positions, and the chronic nature of the symptoms fits with the wear and tear associated with these conditions.

Adhesive Capsulitis (Frozen Shoulder): Although typically presenting with a more gradual onset of pain and stiffness, some cases can have a prolonged course with intermittent exacerbations, fitting the 20-year timeline.
Cervical Radiculopathy: Pain from the neck can refer to the shoulder area, and given the duration, it's possible that intermittent cervical nerve root irritation could cause these symptoms.
Thoracic Outlet Syndrome: This condition involves compression of the nerves and/or blood vessels that pass into the thoracic outlet (the space between your collarbone and first rib), which can cause shoulder pain among other symptoms.

Lung Cancer: Although less likely, lung cancer (especially Pancoast tumors located at the top of the lung) can cause persistent shoulder pain due to local invasion of the tumor into nearby structures. Given the potential severity, it's crucial not to miss this diagnosis.
Cardiac Ischemia: Referred pain from cardiac ischemia can sometimes present as shoulder pain. While the intermittent nature over 20 years makes this less likely, the potential consequences of missing cardiac disease make it a "do not miss" diagnosis.
Spinal Cord Compression or Lesions: Conditions affecting the spinal cord, such as tumors or abscesses, can cause referred pain to the shoulder. The long duration doesn't rule out these conditions, especially if they are slowly progressive.

Polymyalgia Rheumatica: An inflammatory condition that can cause widespread muscle pain, including shoulder pain, though it typically presents in older adults and is accompanied by other systemic symptoms.
Sickle Cell Disease with Chronic Vaso-occlusive Crisis: Although rare, individuals with sickle cell disease can experience chronic or intermittent pain due to vaso-occlusive crises, which could potentially manifest as deep shoulder pain.
Ehlers-Danlos Syndrome: A group of disorders that affect connective tissues supporting the skin, bones, blood vessels, and many other organs and tissues. Some types can lead to chronic joint pain and instability, potentially causing deep shoulder pain.