Now that they are experimenting with allowing the rift controllers to manipulate both the stick and throttle in the TF-51D simultaneously (and maybe all the older warbirds?), I still hope they will allow two buttons or switches to be held at the same time, which is needed for both the TF-51D and hornet start-up sequences.
To my surprise, I was able to land (poorly) completely HOTAS-free, just using the controllers and my pedals, with no other peripherals (mouse, keyboard, etc). It's a cool novelty, but ultimately, I don't think the controllers will be able to replace a true HOTAS.
I personally find using the controllers to be more immersive than using the mouse for non-HOTAS functionas, but in the end, I suspect we will need a glove-type solution that you can wear comfortably without imparing HOTAS use.