I would suggest build it like the Apple store in New York City on 5th avenue. All underground with the glass cube as the entrance above ground. That NYC store is simple but elegant on the outside and immense on the inside. The glass cube would be a much closer fit with the design of the other buildings at Federation Square too.
Well, you clearly don't watch Australian Open tennis every year like I do. Based on the tennis players that seem to drop like flies in Melbourne's 100 Fahrenheit/38 Celsius heat... No, you wouldn't want to build the equivalent of a hothouse/greenhouse in a sunny public square. Would an unshaded glass cube work well in Desert Hot Springs, where you live?
Yeah, Apple loves lots of glass, but if the climate requires that the glass be well-shaded, then that's what they'll have to do. Just take a look at the photos of Apple Park. Same pagoda-like deep eaves. Could it be that, ornamentation aside, the design of pagodas is practical in nature?
As to the rest of the controversy? It's completely predictable. To some, change of any sort is unwelcome. To others, it's a matter of sticking a finger in the eye of the foreign invader. It wouldn't matter whether it was the embassy of an totalitarian communist, colonial, or fascist government, or a retail shop for a giant multinational, either the right or left is going to be agitated. A design that might be moderately disliked had it been proposed for a museum or university becomes a target of hatred if the occupant is unwelcome.
And yeah, that awful, awful Apple logo. You'd think the symbol was a dagger dripping with blood or a black swastika/hammer and sickle on a red background, instead of a blandly white piece of fruit with a bite taken from it. Still, I'm sure at least one cartoonist has drawn Snow White's wicked witch with an Apple logo in her hand.
Well,whatever. It's easy to feel really small in our grossly over-populated world. When an opportunity arises to make some sort of an impact, any impact, people will try. Hell, look at what's goes on here in this discussion forum! Should it be any different out in the real world?
While most local construction/building/development laws are rooted in public safety and attempts to rein in urban chaos, the public has given itself a say over how things look, too. Give 'em all a break. Apple will get what it wants - a highly visible store in a densely-trafficed tourist district, and the locals will get their chance to push Apple around a bit before the final deal is done. Just ask the people of San Francisco and Washington, D.C.