I’m an Aussie - congrats on snagging the trip of a lifetime, and free airfare to boot! Stretch as long as possible. Two weeks is just not enough time. Any way you could telecommute for a few more days?
You’ll lose 3-4 days in travel (remember, you lose a day getting there, in essence) and recovery. The trip is brutal on sleep patterns/jet lag. Expect to be up in the middle of the night for a few days.
Are you leaving from the West Coast or East Coast?
Here’s the deal: Australia is the size of the continental U.S. You wouldn’t try to see all of America in two weeks; you’d concentrate on a couple of areas and hope to do the rest later. Problem with Oz is that most people never get a later. Hence the encouragement, again, to get more days for your trip.
In Sydney: if you’re adventurous, the Sydney Harbor Bridge climb is unforgettable. Downtown - walk from the Opera House to the botanical gardens. Also, Taronga Park zoo (city is the backdrop), the Rocks historic area downtown, Manly Beach via the ferry, Bondi for the surfers clubs (it’ll be spring then; you’ll have perfect weather) - beaches in general are sublime. Darling Harbor for shopping as you’re prepping to leave.
The closest other city is Canberra, but even though I spend my formative years there, honestly, you can skip it.
I’d try to get north to the reef, but it’s a long haul - about 12 hours. You’ll probs have to pick either the reef or head in the other direction, to Melbourne. Melbourne is about eight hours overland; longer back along the coast road, which is worth doing.
Unless you’re heavy into the ocean/snorkeling etc, I would pick the other direction, for Aussie-specific sights. See Melbourne/ drive the Great Ocean Road/ take a (car) ferry to Kangaroo Island. My parents had their honeymoon there and it is AMAZING - penguins, seals, wallabies & roos, koalas etc - nature to die for.
Skip Uhluru. I was born in the middle of the Outback and while it’s also stupendous, again, you can’t do it in the time allotted.
If you head to Melbourne, you MUST try to catch the Aussie Rules footy. You will thank me 
Let me know if I can be of more help. I LOVE my country 
ETA: Almost forgot: Borrow or buy Bill Bryson’s “In a Sunburned Country.” Best book to distill the essence of Australia for an outsider.