Walt I would be happy with option one but if the goal is to give players more control over their ship it feels like a half step. Having to aim and fire your weapons with the mouse cursor would make combat a lot more engaging and raise the skill cap in MP. As others have mentioned players would be able to lead there shots more accurately. Also players who spend more time piloting a certain ship will become more effective at using it, which is good I think. Implementing a manual control method that utilizes a mouse is worth it for the game I think, for me the biggest issue with the combat is that most encounters are spent watching the battles and not piloting in them.
I have an idea for the control method and want to know if it's something you'd consider.
I think it'd be best to have a mix of both options you proposed. Manual controls should utilize WASDQE and lock onto your ship whenever they're pressed, but your mouse cursor should also aim your weapons and turn your spacecraft (D and Q should also rotate the craft). With this manual control method I think adding one option would help a lot, which would be to toggle whether your mouse cursor aims your weapons and stears your ship, or just aim your weapons. This would be good for broadsider designs and others like it, and you'd still have all the maneuverability you need with the directional keys.
I think this idea would work well, what do you (and anybody else) think?