Alrighty, playing through it right now and I'm in a bit of a rush so this is going to be a bit listy and/or *****y, so sorry up front.
Why do I know how many containers I have to blow up to clear the debris field? I think you can hide the directive counter behind a second event (like, set the directive to 'is-event-true-delay (blow up containers event)
And on the warheads part: I have nothing against them being cylon nukes, but why would my targeting computer know they are cylon missiles?
Having gotten to the end, I think it would be better to have to disable the ftl first off then clear through the field.
How many people fit in a raptor?
Overall its solid though.
Deliberately trying to break stuff play-through:
right off I fired a whiplash into the engine which stopped the ship and broke the mission. Maybe either guardian them so they can't be destroyed, or make the ship blow up (and presumably fail the mission) if the engines are destroyed. Likewise, the ship never tries to jump out.