Hmm. Well the missions seemed kinda awkward to me, the main thing being huge waits all over the place with nothing to fill it. Though I did experience some funky sexp turbulence in the first mission where the Ravana got destroyed before the escort cruisers, and then everything went downhill from there as the pilots started screaming about how the Ravana's powering up its beam cannons and it's tearing them apart. The mission concepts themselves though were pretty cool.
The story, on the other hand, was very cool. However I do think there were some problems with its execution, for instance
the mind-controlling Shivans, while an interesting concept, would have worked better if the Vasudans didn't do the whole 60's scifi act, maybe if they'd just gone silent and cut off their communications or something before warping out. Also I think whatever happened onboard the derelict in Betelgeuse could have been handled better - their screams were kinda unconvincing, again sudden silence would perhaps have a more eerie effect... but it's your story of course, just some suggestions.
The only other gripe I have is the whole humour thing (Lampshades?

). With a bit of polish this could turn out to be an awesome campaign.

In short, pretty much what Goober said.