The main difference between these two places would be the terrestrial experience; the GBR is best done with a 4 day to 2 week liveaboard trip running out from Cairns of Townsville. These are fantastic, but are totally ship based and well offshore on the outer reefs.
Fiji is more island based, with shorter trips and land based diving available. The question is really whether you want to spend your time out of the water on a boat or an island.
Personally i'd go for a good long trip on the GBR, but i'm biased
I'm sure Fiji is also completely brilliant, and you will not be disappointed no matter which you choose.
Sharks are a non-issue, harmless unless you are spectacularly unlucky (and probably a bit stupid as well). They are also great to dive with, especially on night dives when the white tips come out to hunt on the reef.
The only concern with jellies would be the box jellyfish, and irukanjii, which are both in northern australian waters between around october to april or so. They are also confined to inshore waters and are not an issue on the reef because they are largely absent, and you are almost totally protected with wetsuit, boots, etc.
Ultimately, its a question of personal taste, both are brilliant.