Darn, the mission I'm working on (my first) has some violoations to #1 and #2. 1 out of 3 isn't bad right? Although I could always include ESD still.
Just kidding, but in all seriousness I'm not trying to be cliche at all with the mission or overuse those elements because I understand the over use. The Borg references are only for setting reasons and only appear in dialog, at no point does the mission see a drone or Borg ship of any kind. And while I could possibly use something else besides the ship as the catalyst for my story the ship explanation makes the most sense for the story. In the end though the ship and crew have long been gone, it's not an active find the newly missing ship type mission and it is just a catalyst for the story, not the story itself.