Hi, so I'm one of the volunteers on the game, though my role is somewhat limited to...mostly the balance side of things. I can answer two of these however.
Something I learned from another game I play is that personal shield bypass (like fusion reaction of the standard bombers) contributes nothing unless you kill the hull before the shields are down. Is this intentional to discourage "death balling" bombers mixed with other ship types?
I don't believe it was intentional for this, no. The bit about contributing nothing is very true, I had that realisation a while ago and did some changes to a lot of structures and the Bombers themselves to work better with it. They are in my experience however, a unit that does do better if controlled separately and specifically to make use of that ability, so in a way I suppose they do unintentionally discourage deathballing.
The default primary color for the human resistance fighters is very hard to see against the tool-tip background
Any particular colour come to mind that works for you? Mentioning a specific one that's good would be appreciated, as I am a bit colourblind and might pick a horrific one, but not required.