I'd like to propose a different way to refit ships in comparison to GC2.
In GC2, you can refit ships everywhere, anytime. It takes one turn and money and they are back. That disturbs me a bit, because it's not very realistic. How do I get the cutting edge military technology to the middle of nowhere? Where do the infrastructure for the major refit comes from? Replacing engines and weapon systems is nothing your ship engineer can do just with his toolbox, you need a little more equipment than that.
My proposal: Just allow ships to be refitted on colonies and star bases.
On starbases: the base need a ship refit module (a stardock) where you can refit the ship for money (like in GC2). The base has the infrastructure and can protect the ship (if armed) during refit because the ship stays on the star bases tile.
On planets: Only colonies with a star port can refit, and refit there could either be GC2 like (pay your money) or MoO2 like - add a "refit ship" task to the star port's build options, so the colony can refit the ship with its military porduction points. That may take some turns, depending on the tech level changes + ship size (like the money I need in GC2 for that) and depending of course on the production points of the colony. This would help refitting older ships without bankrupting you.