The most obvious point is the whole usability. As bad as the default X-Plane 11 and MSFS atc are they are easy to use and intuitive. I need 10 buttons to control the whole ATC :1-0
I only need 1 hotkey to use PF3 because I utilise the VCP
Comparison: When I'm at cruise MSFS offers me to ask for a different altitude. So I just press buttons 2 or 3 and then I can press 1-9 to actually choose it. I don't need to find the Hotkeys for that function because I don't need to. This is pretty important in VR since you can't see your Keyboard. So pressing multiple buttons at once is not practical.
A proper context sensitive menu works a lot better. You can of course still keep the hotkey option as it is on top of that.
Well I don't use VR nor will I, as I suffer from vertigo and the two don't go together. However, I would have thought the best thing would be to use vice recognition, then you won't need any hotkeys at all.
Also Navigraph integration should still be done: A use case: When flying towards an Airport I like to tune in the ILS frequency after looking at the corresponding Navigraph chart. This works flawlessly in the default ATC. As soon as I am in range The message starts playing without me needing to do anything else after tuning in the position.
PF3 doesn't use its own frequencies, it uses the data from MSFS, so I'm not sure I understand your issue here. Obviously you have to rebuild the PF3 database to ensure everything is in sync, especially after MS release an update.
To test this I started a flight in the TBM 930 standing at EDFE and tuning in 118.730 for the EDDF ATIS. PF3 simply does nothing.
On my system the ATIS info for EDDF is as follows:-
So no, if you tuned to 118.730 PF3 would not recognise it. Also that's an 8.33Khz frequency which is not currently supported by PF3 yet anyway so you would have to use 118.72 as shown above