A striking feature of the Restoration Navy was the suddenness that morale could collapse in the face of adversity. The foremost example was the loss of the Royal Prince at the Four Days Battle. I believe that Sir George Ayscue was suspect as a naval leader, so I partly atribute the debacle in the Four Days Battle to him. After the Royal Prince grounded, the crew panicked and became unmanageable. A stronger leader might have restored the situation, but Ayscue did not. He seemed powerless to affect the outcome.
A related example played out much differently. When the Henry, John Harman's flagship at the Four Days Battle was fired, the crew also panicked. In this case, John Harman took charge, rallied the crew and put out the fire. The Dutch were amazed to find, later, that the Henry had been saved to fight another day.
The issue may be partly attributed to the extent that crews were pressed. Many men pressed into service maintained a good attitude and served for extended periods, such as Edward Barlow. His journal is a classic, and is illustrated by Barlow's ship drawings (primitive but good).
Perhaps the real answer is the moral tone set during the Restoration period by the King and Duke of York. They were good men, loyal to the navy, but their private lives were not what we would expect in these stricter times.