For example, if i give some ships an direct order to attack an important target they often or most of the time fight with target in "their way" and don't follow my command to shoot down the target!
As much as I am annoyed and frustrated to no end by this behaviour, especially so since I'm used to blind obedience of units in C&C, Starcraft and so on, I always saw this behaviour in SS as a successful and brilliant implementation of ship captains having minds of their own, making me, as a fleet commander, put their whimsical nature into account while creating my battle plans. Even though this feature is hated, it would be sad to have it gone.
However, seing as there will be actual "captains" implemented in the next SS patch, I think it would be great idea to add "promptitude in obeying" as one of captains skills, so that players could, if they wish to, assemble a cadre of 100% obedient captains.