Not sure I can add much, given I have not played that much DW, and found your first game background description so delightful, as make any suggestion daunting.
M. Holmes feeding info to Cunningham... Awesome!
I did wonder if at some point you might want to consider asymmetrical forces. If you have ever seen the boardgame Seastrike, an inspiration for Full Thrust's ship icons, you may be aware of the scenarios built themselves from random objective cards, each with points appropriate to how limited the objectives.
They even inspired one fellow to create versions FOR FT.
Maybe down the road a bit...
Doug