The next patch is reported to fix the population miinister.
In a very old, pre-gold patch, the population minister worked just fine -- at least late game. I had various breathing types and the pop minister moved them around well. No planets were depleted seriously, and the transports only got stuck occasionaly.
Maybe the new patch will return the fuctionality the game lost for a little while.
Colonizer is still brain dead, that's for sure.