Australians nowadays don't connect as much with the British royals, unlike the older generation who did. The result isnt because of Mary's "popularity of late"... IMO Mary was chosen over QEII because she's was once one of "us": she knows and lived the Australian lifestyle, know what it's like to live and work in Melbourne, Sydney, has enjoyed the same beaches and sights as most of us etc, whereas the Queen has never done most of the things Australians do.
Does that make sense? Perhaps one has to be Australian to understand, not sure.
Or perhaps the whole Diana thing has affected how trustworthy people view the Queen?