I would agree that, all things taken into account, FS2 is a greater literary work. FS1 does, however, have some things in its favor. Really, it comes down to what kind of story appeals to the reader. FS1 is simple, and, like AV8R mentioned, plays very strongly on emotions of fear, dread, heroism and triumph. FS2 is a darker, more complex story that raises the threat level of the Shivans... to the point where we ask, "In the long run, do we have any hope?" If the series had stopped at FS1, I think that we would never have seen so many fan campaigns, for the simple reason that FS1 satisfies itself, while FS2 leaves us hanging, wondering what will happen next. Truth to tell, very few campaigns actually answer the big question: "Is there hope?". Because an answer epic enough to meet the question seems impossible to deliver.
One reason Derelict is so fun is that it's halfway in between. Yes, the Shivans are back. Still mysterious, still unstoppable. Yet you still get the chance, at least for now, to win, to feel that victory, to see the Nyarlathotep explode. We might be ants to them, but we still bite. Is there hope? We don't know. But for now we can celebrate.
In fact, I would argue that one of the strengths of Blue Planet is that it plays on the strengths of both original games and improves them with top-notch writing. Age of Aquarius is a very FS1-like story but with much better writing: "We CAN win, there IS hope. The Shivans are powerful, but there IS a chance we can get past their threat, if we can meet the challenge." War in Heaven, especially Tenebra, proceeds to cast doubt on that conclusion: "Is there really hope?" The Vishnans, who seemed to be offering us a chance to prove ourselves worthy, begin to look much less friendly. This is part of the reason that, despite a few things that bugged me about BP, I'm a fan and I'm eager to see it finished. Because If AoA mirrors FS1, and WiH resembles FS2, the third Blue Planet just might replace the conclusion we lost when Volition went under.