1. Speeds of ships in instances. Less fun when all age of sail battles feel like a RC Boat battle. There's no natural delay of orders, no natural resistance to movement, no loss of trim during combat. At the moment, with what I point out in 2. and 3. ( below ) it becomes very predictable, mechanic and slightly off.
2. Officer Perks. While they are a excellent concept it is not fun when they interfere directly with the normal flow of combat. It is not fun when a perk becomes mandatory. It is not fun when 1/10th ( 0.1 ) of wind usage, positioning and timing is replaced by a bonus given by a gimmick that can be achieved with mindless grinding.
3. Equipment and Modules. As with the officer perks, they are a very good concept but not fun when their effect in the action becomes overly decisive. It is the sum of the parts.