You’re exactly right there. That’s why I have no real interest in using VR controllers. And would we need ‘foot controllers’ to work the rudder and brakes too 
Resting left hand on yolk and right hand on (or just behind) throttle is how I was taught to fly. Now that I’ve long since been constrained to virtual flying, I have an old logitech joystick, an ancient Saitek throttle quadrant (with one axis non functional), and a set of indispensable and equally venerable CH Pro Pedals. That covers the primary controls nicely and everything else can be done with the mouse pointer … which I find quite okay in VR when you get used to it. Even mixture is manageable with the mouse. I’d say that for VR you need controllers for the primary functions.
For communication, you could look at some of the voice control add-ons such as Pilot2ATC or VoxATC (not sure this works with MSFS). I’ve used VoxATC in the distant past … really took some getting used to, but did avoid the need for using ATC menus in FSX.
MSFS currently has no means of displaying external documents (maps, charts, plans) or of copying clearances and frequencies etc. This is - in my opinion - a huge limitation in the current VR implementation. Easy enough in 2D to switch to another window, but can’t be done in VR. I know there are a few folk trying to come up with work arounds … but if it’s not native within MSFS, I’m not sure how effective it can be. Quite a few comments on this already - vote here!:
After all that though - I gotta say I’m addicted to MSFS in VR!