I have two suggestions for improving the game. The first is very simple: a notification sound when you enter a game lobby. Match search can take long and I'll often be reading websites while waiting. Without a notification sound, the only indication that you're in a game is people talking or the count down sound.
The second idea is a way to make the AI disregard certain ship components. On the ship menu there would be a list of the components with two checkmarks for guns and one for other components. If the captain checks the first mark, the AI will not consider fixing it during its routine and if he checks the second one the AI will not consider firing that gun. This way the captain could confine the AI to a part of the ship. You could then force the AI to remain on the main deck of a galleon or a pyramidion for example.
I think this is a relatively simple addition that will make the AI much more useful. It is completely predictable what this will do to the AI routine (unlike the option to prioritize certain components) and it would not require any tweaking of the routine either.