I'm not terribly bothered because I don't fly Qantas... but...
Same sentiments here, but I will fly QF again one day, not sure when.
3. Economy on the top deck will just be confusing for pax during boarding.
Actually it's not too difficult, SQ manage quite OK to board Y passengers in the upper deck without too much drama, just need signs/lanes indicating rows that need to be boarded upstairs.
Having flown SQ economy upstairs on the A380, as far as economy goes, at least the sort of economy with 31-32" seat pitch, it's pretty good. I'm sure there'll be high demand for these seats on QF, notwithstanding they are most definitely not at the front of the plane, they are the sorts of seats that elite pax will be interested in.