The fate of the galaxy hangs in the balance as the Arecean Empire tries to ascend rather than join the Korx Hegemony. A fleet of Korx fighters are dispatched to destroy their starbases and clear the way for invasion when the diabolical Arcean plan is revealed, sabotage! Korx engineers have been bribed to build ships without life support! Since the leader of the empire's a moron and didn't notice, the invasion can't get out of its home system. Doh! Quick, all reasearch to diplomacy for the quick win!
Apart from that little setback, there are a couple other issues that get my ship designers closer to getting a good look at their work from outside the airlock. First is the obsession with weapons and defense. Why can't I focus on hit points, speed, sensors, range?
Second is their inability to work with core ships, which might be a mixed blessing. I found myself wishing a few times they'd keep scout/constructor lines open too. That would take a lot of micromanagement out of continually strapping new engines on them.