Spme of your problems should be getting over soon, atleast on the reservations side. Both BA and Qantas have now moved over to the same vendor, Amadeus and while BA is more or less fully integrated , for Qantas, process is still going on and should be complete soon. This means that things like Frequent Flyer Data, Adsvacen Seat Reservations etc will be integrated from the same database.
Infact this is one of the major problems with alliances. In the initial days of KLM/Northwest alliances the integration (KLM and NW use two different reservation systems) was far from perfect and there used to be frequent cases when bookings for one airline used to get cancelled by "messages" generated from the other airline system with passengers getting stranded at peak times on heavily over booked flights. Things have now apparently got much better.
Regards