Shamelessly reposted from the 3.04 thread:
 
Can you please put in some code that destroys all (or all but 1) existing pop when a planet is conquered by an incompatible civ?
 
I would define "compatible" as Carbon/Aquatic with Carbon/Aquatic.   Synthetic only with Synthetic,  and Silica only with Silica.
 
It is slightly rediculous,  immersion breaking,  and game-breaking that a race that spends so much time and resource to build more pop gets unlimited instant free pop conversion if they take over a meat planet.    It is only slightly less rediculous (but more amusing) that when a meat race takes over a synthetic planet,  the robots all start having babies.
 
One other thing I think is very silly is that conquering a planet that has an Capital City keeps the Capital City.   This is also nonsensical - if I can have multiple Capitals,  why not just build them everywhere?    I think any conquered Capital City should be knocked down to a Colony Capital.     You clearly have some code to re-designate another planet a civ's capital,  so if a civ loses its capital city it should be easy to just bump the re-designated Colony Capital up to Capital City to compensate.