Some things I'd like to see in a Star Control story:
Right from the get go, Fwiffo is leading a dangerous life. In the early game he's often the ship's only defense against Sylandro probes, Ilwrath, etc... That's a lot of pressure for a guy who, even by Spathi standards, is a coward. I'd imagine Zelnick would have to practically threaten him with death to get him to captain his vessel at times. But if he lasts, it's because he's also good. Damn good. He should be there in the final battle against the Sa-Matra, and I wouldn't mind seeing him save the day, and learning what it takes to be a hero.
I see the seeds for the Black Spathi Squadron rumor, especially if Zelnick retains Fwiffo and a handful of other Eluders. . .
Maybe the black and red paint camouflages or conceals their appearance (to look like harmless probes or something) when they invade slave-shielded worlds.
Also: Just read the first draft. Very nice pace and set-up. I had some pre-conceived ideas about how the mining operations took place so I was a little confused about your description. I never read any of the manuals so I thought everything took place while inside the lander. It does make sense that some people would die while others didn't if they actually got out of the lander. How does the drill operate? I don't think a totally new reader would have a problem, though.
I think you need to watch out for modern-day vernacular that people might not use in the future. Do they know what a Swiss army knife is and do they use it in the future? What do they eat? Who knows what marshmallows are? And there were some grammar errors, such as "whose" vs. "who's", but those are very minor and will be corrected later.
Re: the Pkunk battle. I have only played the UQM port so I don't know what other insults the Pkunk guys said during battle. Do they say all those things? I thought it was just: Jerk. Moron. Stupid. Dodo.
I'm not sure what their place is in the very beginning of the story, either. Did I miss something?
Great work!