Puke:
That is already a part of it.
Pax:
ie: Fighters.
That option would certainly screw the AI over. But, since we are going to ignore the AI, that isn't too much of a problem.
Taera:
Ok, no problem. The original plan was to steal everything needed from other sources.
Another idea:
Not all systems will be Planets. Some will be other types of planes, like the 4 Elemental planes. There will be special "planets" in them that will make very poor colonies, with 1 mil pop and 1 facility. The system will have a lot of stars in it, so that one Mana Shrine (or whatever) makes a huge amount of mana (the Elemental Planes are raw magical energy, after all). Colonizing the planet(s) will yeild special technology (spells) that is related to the plane. Like the Plane of Fire could give Improved Fire Balls, or something.
Technologies are going to represent both actual technologies and spells.
No "Normal Planets" will have ruins. There may be special planets called Wizard Towers or something that have ruins on them that give a tech. But they will have 1 facility slot, and 1 mil population.
I think that 1 M population might be better viewed as 1,000 instead of 1,000,000. Then, it could represent the labor force that is loyal to your empire, or something.