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Maybe have shields as a later tech, most races in Sci Fi have to research shields. It makes sense for earlier ships to be fragile things.
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I totally agree with you concerning the star classification and rarity, only issue would be how much processing power would be needed to simulate...
Galaxy map graphics aren't that important to me. I like the system used in Aurora, which is very ugly to look at but is chock full of information....
I'd actually prefer a 2d map, I find it easier to navigate and plan my moves. I like the idea of a huge galaxy (1000+ stars) with range limits...