I think you've hit the nail on the head there. Any Super Hornet upgrades will most likely be in the form of improved weapons, communications and data-links, electronic warfare systems and perhaps sensor improvements. Some upgrades have already been announced, including:
ADF has already announced it's intention to acquire new air to air weapons for the JSF and Super Hornet in years to come.
RAAF has already announced it's intention to acquire the Laser JDAM capability for the Hornet, Super Hornet and JSF.
They have announced an intention to acquire the improved AGM-154 JSOW C1 to equip the Super Hornet and the JSF.
They have announced an intention to acquire a new maritime strike weapon system to equip JSF and potentially the Super Hornet in years to come.
They have also announced an intention to acquire the Small Diameter Bomb 2 for the JSF and potentially the Super Hornet in years to come.
I suspect that as the Super Hornet moves through it's RAAF career, it will follow standard-wise the USN for commonality and capability benefits. I envisage at some point an MLU (mid-life update) will be undertaken and I suspect we'll see radar, ATFLIR targetting pod, combat avionics systems (sensor fusion, distributed targetting etc) Electronic Warfare and data-link upgrades as a priority for the Super Hornet.
RAAF has also announced an intention to acquire a AGM-88B HARM and an AGM-88E AARGM missile capability to support the EA-18G Growler in-service. It would not surprise me if those weapons were to be integrated on the Super Hornet fleet as well.
I think you are spot on about your assessment of the path the Super Hornets will follow through their service lives, it makes a lot of sense to 'piggy back' onto the USN path for the Shornets for a whole lot of reasons.
I remember reading at the time on the introduction of the Shornets, that the RAAF was very conscious of following the USN configuration for those aircraft to ensure there was a smooth and trouble free entry into service, especially at that time when they were intended to operate for approx only 10 years.
And in weapon fit too, whilst the Classics were armed with ASRAAM and JASSM, the Shornets are cleared to carry AIM9X and JSOW and also different targeting pods too, they wanted to avoid having to integrate weapons that the USN didn't use, despite the fact that ASRAAM and JASSM already being in service with the Classic fleet.
But I do wonder, now that the Shornets will be in service for double the original time, eg, at least 20 years, which is approx 10 years operating side by side with the F35, if there will be any deviation from the weapons carried compared to the USN Shornet fleet?
There appears to be commonality between the F35A and the Shornets in weapons fit in that both will carry AIM9X, AMRAAM, JSOW and the J series bombs.
In regard to JASSM, as I understand it the F35A will be able to carry it, externally not internally, will the RAAF integrate JASSM onto the Shornets when the Classics retire despite the fact the USN doesn't use JASSM?
The other area of difference is Anti-Ship weapons, the common weapon initially will be JSOW, the Shornets carry Harpoon, but I haven't read anywhere if the F35 will be armed with Harpoon, if it was it would probably be external.
Then there is the possibility of the Norwegian JSM being acquired for the F35, which will fit internally too, if it is, will it be fitted to the Shornets even if the USN doesn't use it?
And there is also LRASM-A, based on the JASSM, if this is considered for the F35A as an external long range Anti-Ship missile, would it also be fitted to the Shornets too?
To me, these questions highlight one of the other problems for the RAAF in having to operate a 'mixed' fleet of fast jets for a long period of time, compared to the desire to have one common platform and also a common set of weapons too.