While it does start to drift a little from the original topic, perhaps a solution to the OP and future issues could be the introduction of storage facilities, one for minerals, one for fuel, one for missiles and one for everything else. They need not require any population nor upkeep to keep the micro work down. But it would mean you can't just pile up mountains of minerals all on one world etc, with the new spoilers coming too it would mean those offworld colonies used as storage depots need to be looked after both in the RP world and game mechanic one.
I can see where some folks might not agree with this being a good idea. So simply add a game option similar to the free maintenance option we currently have, either "stuff requires storage/stuff can sit anywhere".