Slight adjustment suggestion:
Presently the commander auto-assign, when it works correctly, assigns warship commanders based on Crew Training bonus, then assigns a bunch of other things including auxiliary command roles, and then fills remaining warship commands based on Reaction, Engineering, and Tactical bonuses.
I would suggest that instead Reaction should be the primary and first skill bonus for warship commanders, and Crew Training grouped in with Engineering and Tactical at the end. This is a very simple change but I think it works better with how C# handles commander roles compared to VB6.
The reason being that each of these skills only give 50% of their benefits from a ship commander, but 100% from the associated command module officers. Reaction however gives 100% of the commander's bonus as there is no module for it.