My biggest suggestion is get rid of Rumors and Propaganda and Sabotage as empty offscreen dicerolls and replace them with activities that make use of your ship and build. For example, instead of a planting a rumor to improve relations, it's replaced with "sponsor a diplomatic delegation with X" which spawns a diplomat ship. The expensive option could have a whole armada of escort ships protecting the diplomat while the cheapest option sends out the diplomat by their lonesome and it's up to the player alone to see them to their destination alive.
My next suggestion is to get rid of command points and instead increase module capacity with ship sections that function like the "bags" system. So for example the player's ship starts with Mk1 warp nacelles that only have capacity for one heavy thruster module, but can upgrade to Mk 2 which fits one heavy and one light. So you'd have things like Engineering that fits power generators, Bridge that fits crewmembers, and so forth.
And if you go with my second suggestion, I suggest instead of switching between ship "classes" each with their own separate model that you have modular ship models displaying these sections. So you'd have a central "hull" section that forms the main model of the ship and each successive larger hull section has a larger model, and the things like warp nacelles and weaponry models would be attached to the hull the same way you display armor and weapons attached to a character's model in the fantasy games.
Thanks for hearing out these suggestions!