I played through a version of this scenario that I tweaked myself and I managed to conquer the Aborigines after something like 300 turns or so.
My changes: I removed traits and bonus techs from the Aborigines. They have such a huge advantage of size, they don't need anyother help. Also I gave the English enough free techs to brings them up to the late Medieval Period, through Magnetism and Metallurgy, essentially. And I gave them enough starting money to pay for all those units for a few turns.
My strategy: I immediately founded cities on the rivers North and South of the starting city. My next city I founded to the West right in between the iron and saltpeter. I then built fortresses on each of the hills surrounding that city and put musketmen in them. Once I had a few small stacks of cannons, I was able to withstand the hordes of aborigines that eventually came down on me. I popped a Leader, got an army, and started razing their cities all around my enclave. I captured their capital because they had built a wonder, and then declared peace. From then on it was only a matter of time as I built cities in their ruins, built goodly amounts of cavalry and laid waste to the rest of their cities.
My comments: Obviously an impressive amount of work went into this so far, but it isn't really playable out of the box, as it were. Once the English have been given their free techs and enough money to pay for all those units, though, it can be played, and it is sort of fun playing pound the nasty savages.
My suggestions: The scenario does have a very narrow focus, though. I think it might be a neat idea to broaden the scope of the game beyond the historical. Why not let other of the European civilizations try to colonize Australia as well? You could replace all the non-European civilizations with Aboriginal super-tribes, divided up into alliances as I suggested before. Then just plop down the Europeans wherever you like, and see who comes out on top?
Pat