Personally, I think it would be worthwhile to rethink Hunter's classification as a 'Frigate' - especially if her cell count ends up being on par with Hobart. Keeps things simple, and better aligned with classifications in our region.
If its a destroyer, why do we need Hobarts? Best to get rid of them if we have 9 other destroyers. So goes common thinking..
I think its useful to have two different types of ships. It makes their role clearer to others, even if there is some capability overlap between them.
Given the direct things seem to be taking the Hobarts look like being more closely following the US destroyers with AEGIS and possibly Spy6. They may be slightly quicker (although lots of disclaimers, and the efficient speed of the hunter is likely quicker than the Hobarts) and probably a more obvious choice to integrate into US carrier fleets.
The Hunters are a bit more sovereign, with the CEA radar, which may create a bit more work for weapons and fleet integration, upgrades, perhaps. They will certainly be more flexible, with more flex space and a larger helo landing capability (chinook!) and a stronger ASW capability.
Even if they carry similar amounts of missiles, we don't know exactly how that works. I doubt the Hunters will get more than 48 strike Length VLS. If if they do, I doubt Australia is going to buy a bunch of SM-3 for final weapons integration and shoot a couple of ICBM's or sats. So Hobart's may end up being focused in that area, if SM-3 get acquired.
Its very hard to compare an existing in the water ship like the Hobart facing its first upgrade, with a ship that is not in the water, and whos details are still yet to be confirmed. Are the Anzacs more capable than the Perth Class destroyers? Should the Anzacs be called DDG's too? Seems like murky water/slippery slope.