Maybe Imperium Galactica. It's the spiritual successor to Reunion and features a storyline where you become captain of a small fleet with a few planets under your control. You have to construct buildings, research techs, move your spaceships around to discover new planets (and aliens) and of course, every spaceship can be individually refitted with scientific inventions. On top of that you must manually fight battles on the planet surface when you conquer an alien planet.
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