Hiyas,
One of the first things I do is go into GalCiv3mapdefs.xml, and change the value for
<ReduceStarSystemBoundarySize>5</ReduceStarSystemBoundarySize>
from the "0" it is at initially, to the "5" you currently see it at.
the line is towards the bottom of the page.
This gives the density a more "organic" feel, at least in my mind.
This likely doesn't address your issue of "dead worlds", and I entirely agree with your resource rarity complaint.
All things should not be treated equally if one is rare as hen's teeth.
If memory serves, there was a post about lanes in solar orbit being "full" when they were in fact not, affecting planetary density.
Perhaps the same is occurring with "rare" minerals?
The above fix is not mine, I found it here on the forums months back. The original post warns not to put the value above 9, or you'll cause crashes due to solar overlap. I personally found 6 to be too dense, impacting my ability to position starbases to such a degree I had to turn it down a notch.