Since my AUS passport is nearly full and still has 5 years to run I've taken to using my UK passport for all my trips now. So I show that at check-in in Australia but show my AUS passport at immigration.
Only issue I've had is flying direct from the US to AUS because I entered on my UK passport I had to be shown to have left on the same passport; however they needed to enter my AUS passport details to show that I was eligible to enter the country.
Last time it took UA about an hour to sort it out however when I've done the same with QF they've obviously been through the process many times before and were able to sort it out straight away.
So that's my only two cents worth about it!