An idea that came to me (sorry if it has been suggested before) is to use different coloured dice for the individual dice of the engagement roll (for Secondary Missions). This could be used to give some idea of why a particular mission succeeded or failed (or ignored if you prefer). e.g. Loyalty +1d (green), Intel +1d (blue), Scorpion Siege Engine +1d (red). Depending on which ones come up high/low it gives ideas for the narrative.
I guess you could use it for Primary Missions too?