First off, I love this idea! Second off, don't worry about "balance"; think of this as a way to test out mechanics that Alex might well want to put into the game.
Things I'd like to see:
Atmospheric Processors: Temporary. Huge machines convert no-atmosphere / bad atmosphere (Toxic, Polluted, Radiated) to a neutral state. Should take 1 year and 5 million Credits to build.
Soil Creation: Temporary. Nanotech devices gradually build a layer of viable top-soil, allowing a planet to be farmed. Improves farming by +1 or sets to 0 if less than 0. Requires a planet with a breathable atmosphere, 1 year and 5 million Credits.
Planetary Intelligence Agency: Permanent. Eliminates Path incursions and greatly improves resistance vs. Pirate raids. 3 months, 1 million Credits to set up, costs 25K+ thereafter (whatever's roughly balanced for a Size 5 Colony, essentially- by Size 7, it shouldn't be a big cost).
Gravity Control: Permanent. Installs grav devices throughout the Colony, removing the penalties from Gravity. 6 months, 5 million Credits, but 10K (i.e., cheap) to maintain thereafter, as it uses up an Industry slot.
Tectonic Stabilization: Temporary. Using hypervelocity kinetic strikes, the tectonic plates of the planet are carefully shattered in a controlled way, greatly reducing earthquakes and other problems. Removes "unstable" penalties. 1 Million Credits, 2 months to build. (should be pretty cheap, this isn't terribly common).
Biocide: Temporary. Masers and massive sunlight reflectors are used to burn away harmful flora and fauna, along with the use of nanotech biocides, to make the planet 100% compatible with human-friendly lifeforms. Removes "biohazard" penalty. 2 million Credits, 3 months.
Oort Cloud Bombardment: Temporary. Drones are sent to the Oort Cloud to collect water ice chunks and drop them on the planet, greatly improving the amount of surface water on the planet. 5 million Credits, 6 months. Removes "arid" penalty, or if the planet is normal / Terran, can convert to a Water World!
Manufacturing Ring: Permanent. Builds a ring of manufacturing facilities orbiting the planet, greatly improving Accessibility and production. All Industries get +2 production and Accessibility is improved by +2 as well. 10 million Credits and 1 year; costs 100K+ (whatever feels reasonably balanced for Size 7 Colonies; this is an end-game item).
Hyperspace Detectors: Permanent. Builds sophisticated new Hyperspace detectors, greatly improving the sensor reach of fleets in this System. Basically, a planet-based way to build the same sensors usually installed in space. 500K to build, 15K to maintain.
AI Farm: Permanent. Uses "tamed" Remnant tech to gradually replicate AIs left in this planet's inventory, for an endless supply over time. 20 million Credits and 1 year to build, 500K to maintain. 3 months for Gamma cores to replicate, 6 months for Betas, 1 year for Alphas.
Military Construction Yards: Permanent. Special high-speed manufacturing facilities are built for purely military use. Accelerates production of military vessels for local fleets by 100%, reduces D-Mods by 2, increases fleet sizes. 5 million Credits and 6 months to build, 200K to maintain.
Marine Training Facilities: Permanent. Trains Marines and other ground forces in large numbers. 1 million Credits and 3 months to build, 100K to maintain. Builds 100 Marines / month, plus Armaments / Heavy Armaments. 50K to maintain.
Cloning Center: Permanent. Clones and artificial-birthing facilities greatly accelerate population growth. Gives Colony a constant growth-rate of 2% before any other factors are considered (i.e., additive). Improves growth, but the clones are harder to integrate into society. 10 Million and 6 months to build, costs 25K and -2 Stability to maintain.
Basically, put in tools so that players can:
A. Gradually fix up their worlds, at a cost in time and Credits.
B. Use their Credits to build end-game content.
C. Prepare for the final form of this game, where we're hoping that the Factions are dynamic and also able to make use of these kinds of things.