Well, many of these missions have a
too short time limit. The very first one, for example. You can't get to the system and destroy the death gliders before it times out. You
must use warpmap to get there in time to complete the mission. I don't recall how many jumps are involved in the Aschen treaty mission but I might have used the cheat there. I got ambushed, though, so I don't think I missed any events.
BTW, the Aschen system still shows as 'neutral' on the sector map (green) while the Tollan, who refused an alliance, show as blue. Something not edited right?
Also, the Aschen gave me a sample
Blister beam at first visit, but they actually used
Rupture beams when they showed up to fight. Another missed edit? Haven't seen any 'Blister' beams since that first one, and I've scavenged a lot of Aschen wreckage. Got some nice Plasma Torpedoes out of it.
I managed to defeat both Anubis and Apophis by heavy use of fighters. I even scoop up dropped Aschen fighters and use those. Carriers aren't very smart in this game, they just charge right into close combat & get stomped. Maybe something in the AI could be tweaked?
About the slots: How about separate 'crew' slots over to the side then? You could make a special slot type for only those crew objects. That way, they wouldn't be usable for regular components. But you'd get several more useful slots on the ship itself.