I've been playing this game for a couple of months and it occurred to me that upgrading Boffs isn't possible at all really. They get no real development as characters once you pass the faction campaign, they don't really have a role in Admirality, Assignments, or R&D.
So why not create a system wherein a Boff's position within the Assignment, Admirality, and R&D systems upgrades their Traits to the next level? Why not add like one or two slots for Boff Personal Traits and add in a Genetic modification mechanic allowing you to isolate traits from one and apply them to the other?
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A lot of this information is in the game, and they stagger it to when it becomes appropriate, but yes, it's not obvious in the odd case. The game goes out of it's way to highlight stuff, and folk still skip/ignore it
I knew about the upgrade thing though because of the empty boxes left for unlocks but not their full scope. it's just like how the phoenix store is hidden, there are these weird things that the game does that it shouldn't.