One idea would be to add a Racial Trait, call it something like "Industry Development".  Each colony contributes a certain number of Industry points per turn (based on population and racial Industry Development).  Players then select an uncolonizable planet (or Asteroid Belt) in the same system as a colonized world.  Once enough Industry points have been acrued, you can then choose a facility to construct at said Planet/AB.  These facilities can give bonuses to system Production, Research, Economy, Happiness etc, and can continue to be upgraded throughout the game as the player gets more Industry points.  You could give these planets/asteroid belts certain bonuses in order to encourage development of the different types of facilities, and constructors could be sent to them to provide defense or other bonuses.  This would give the game (I believe) a much greater sense of an "alive" universe, with more things happening in developed systems, more opportunities for tactical strikes against your opponents (these facilities can be destroyed/raided by enemy ships), and open the door for more Ideological tennets.

I disagree that inhabitable planets don't contribute to the game. I think they indeed serve important functions in terms of making the game fun:

1. They make the solar systems more realistic.

2. They make the process of discovery more fun - the moment the fog is cleared by your scout to reveal a planet is like opening a lottery ticket. You rejoice if you find a good planet and you are disappointed if it is a dead world. But these are two sides of the same medal - you can't have one without the other. If all planets are useful, there is no disappointment in finding a dead planet but there is also no fun in finding a good one.

3. Beyond the moment of discovery, dead planets and low quality planets give high quality planets even more value - just by there mere presence they show that good planets are nothing that should be taken for granted.

Now would it be fun to have some kind of tech to make use of some of the dead worlds? Surely. But don't go over board with it - if everything in the galaxy is useable, it is just crowded and the player doesn't feel accomplished to have found and secured the valuable things.

I like the Distant Worlds resource system, and I wish GCIII would add some of that flavor. When we become spacefarers there will be very few planets that won't provide resources to be mined and it would be great to include mining for specific planet and asteroid resources.

Distant Worlds does not have the personality of GCIII but little things like having to wait for a freighter carrying the silicon to complete that destroyer adds a lot of character to the game.

My opinion on the matter is this. Not all planets out there are usable. The actual amount of usable planets in our universe is small by comparison to those that are uninhabitable. I think that given the adjustable settings change this ratio I can say what we consider realistic is possible. What I think would be an amazing alteration would be needing to survey planets to determine habitable or not habitable. Sending a ship to survey planets would add alot of ship management potentially, but I would like the idea of needing to in essence research each planet on arrival to gain statistic on it. This could help slow down the mad planet rush at the beginning of each game. If the AI logic of survey ships was expanded upon it could factor in Uncharted planets to survey. Again just my opinion but at that stage you could use surveyed planet information in trade and treaties.

My opinion on how to deal with uninhabitable planets is this.Have a scientific exploration landing party type ship in. Allow the ships to go from charted uninhabitable to charted uninhabitable spending X amount of turns on each to search for extreme worlds, potential mining opportunities, or find ancient ruins.

That is what I would like to see added to extend the growth process of finding and colonizing planets with the added potential of having random events occur on any planet that is not habitable.