Currently the default population assignment seems to assign new population in a system to the planet with the smallest population. Could we have the default assignment instead go to the last planet that was manually assigned population, or failing that, the planet with the highest FIDS total per population?

There is another discussion about that here:

http://forums.amplitude-studios.com/showthread.php?3353-bug-with-no-system-AI-selected-population-still-gets-moved

I am pretty sure that the AI moves your pop to the planet with the highest production per population, without telling you. This is very annoying for early systems, when I am trying to build food, not pop.