The transports used in trade are also used for moving population around. Unless there is going to be a future combat role for these ships (and I don't really feel like there should be), then I feel like the main player controlled role of shuffling around population is too small for a God-Emperor. It seems out of place with most of the other things I find myself doing. The decision to move one million snakemen to an island world in order to get more use out of it is definitely an important high level decision. The manual orders to load and unload the population are not.
As it is, you can't select the race you want to load, so the process gets annoying as you bring in multiple transports to pick up people until you get the race you want to move. If the system stays as it is, that part would need a new interface to allow for picking the species you want out of a list.
Instead, I propose that once the new planet management overview system is in place, that some method of ordering population moves be implemented from that screen, and that transports in the trading pool implement the move behind the scenes. Perhaps add a small monetary price, to reflect nominally independent captains being forced to do this unprofitable task?
Trade raiding has been mentioned as something going in eventually, and this could work with that by allowing that kind of raiding to intercept/capture a civilian population transport, allowing the captor to divert the population to one of his own worlds. This is the main possibility that we have with transports in tactical right now that we would lose out on.