The game itself doesn't need a story to be interesting. While sure, there are some 'story elements' you could say though more background of characters than anything, it really could use more events and the ever present 'missions'. Go out on a mission with one of the gals, gain friendship or such if warranted, or have lewd as fuck sex scene while tracking down the Brotherhood.
Imagine having Jubes on her knees topless or fully naked, sucking us off in the heat of things before say... Wanda, or Boom Boom from the brotherhood show up, or hell maybe intro Wolfsbane and they catch us in the act and get turned on by it. Which naturally would end up adding more to the harem in fun ways.