Well it's certainly a decent flash and you shouldn't feel so dissatisified! I agree with you about swfs though, i've always had difficulty synching sounds and exporting things properly. You're art style is pretty nice and you have some decent frame by frame, though there is a real lack of actual animation is this. It almost becomes a slideshow! I also really dislike the use of photographs, it really detracts from the immersion and makes the art really dissonant and distracting. Find one style that works and stick to it, i think you have the art skills to draw everything and have it look great, but perhaps you just didn't have the time?
The concept was okay but i think the execution was very cliche. The music particular made me cringe, the song sounded far too similiar to the massively over used "Escape" by Craig Armstrong and whilst it certainly has an "epic" feel to it , it also undeniably has a commercial and sterile feel to it. To be honest i have dislike for soundtracks in general and feel that a good piece of work should conjure up strong emotions without resorting to telling the viewer how to feel with musical cues. The reaction scenes when the colony gets online where nice but i think it would have been more realistic to see a few people cheering, or atleast some other reaction than just mouth agape eyes wide. Is this a concept you are going to continue with? I think it could be very interesting.