I just finished off 95% of the colony Pickup Orders functionality. I'm sure I missed something and I still have to test it out a lot, but right now a colony can issue an order to allow another player to pickup items at the colony. A message is sent to the other player letting them know this, and he can send any ship he owns to the colony to pick the stuff up.
I still need to work on the UI of the colony end a bit, and item transfer itself still has a good chunk of work to be done, since right now transferring items takes no time to complete. Eventually it will take an amount of time to transfer an item based on it's mass, with the Cargo skill helping to speed this up some.