for the plot how about we start off simple, the most basic part of the plot will be that some time in the future after several fights with the shivans we discover some sort of psudo weakness, specificaly something like there are only a finite number of there forces in our space and if we act quickly we can cut them off from there reenforcements else were. or something similar to that. the whole idea being that the shivans are godlike power and can never be truely defeated, we can through in some bosch subplot in later.
also if we set it far enough into the future it will not nesisarily conflict with any exsisting fan made campain, though this has the disadvantage (or benifit depending on how you look at it) of requireing all new ships, and probly interface art, and sound effects.