Loathe to call this gamebreaking, but it's certainly immersion breaking for me...
1) The issue where food production is so much easier than energy production, seems unnecessary, since it makes upkeep so much harder for machine empires than biological empires, why doesn't every district produce the same qty e.g. 5?
2) Population growth hard-coded to grow only the lowest population species minority on every planet. This is a reason I am reluctant to play any empire that will have multiple species now and entirely immersion breaking.
3) Organic population growth being comparable whether your colony has 5 people on it or 50 billion (numbers abstracted to demonstrate the ridiciulousness).