i never had a problem with it. its a little convoluted but:
-if the borg go back in time and assimilate earth before earth develops certain technologies what would become of those technologies? would they just disappear?
-its always stated that the borg want the biological and cultural distinctiveness of each race it assimilates. why would you completely assimilate a culture at a point when its at its infancy? assimilating everyone never made sense because then there would be no growing. leaving a few hundred thousand to continue the culture makes more sense.