Here are some general ideas I (and some others) have come up with:
1. We should be able to have habitable moons and colonize them.
2. Why do no planets have more than one moon?
3. Why can there only be 5 planets per star?
4. Why are the only habitable planets in the game around yellow stars?
5. There are not really green or purple stars (that we know of).
6. Where are neutron stars, black holes, quasars, etc.?
7. There should be a random event where a star can go nova and wipe out all colonies in a system and make all planets around it uninhabitable.
8a. There should be an absolute limit on population based on planet class. Perhaps 2.00b*(planet class number).
8b. This limit could be raised with technology, perhaps the miniaturization techs.