It's an interesting idea, but I doubt it's going to happen. One of the demands of visual design seldom appreciated by audiences is the need to communicate information quickly and without recourse to dialogue. A dude sitting on a chair at the front of the ship and pushing buttons on a console just screams "PILOT!!!" to the audience in a way that someone in a VR headset wouldn't. Interestingly, this need to communicate information visually is the source of a surprising number of complaints about lore and plot consistency (which incidentally is why I don't take those complaints all that seriously, although that's a whole other rant for another time).
I don't think that those two things are mutually exclusive.
In the WH40K universe you see many examples of pilots connected to their craft (in a rather grotesque manner obviously, because it's WH40K...)
and it's very obvious what their job is. Clicking buttons and using a flight stick, is simply not efficient enough if you need to react against futuristic drones,
VI's, AI's, and the realities of air/space combat in speeds that far exceed what we can imagine today.
One of the staples of Shadowrun (and cyberpunk IIRC) is the idea of weapons / vehicles / computers / aircraft connected to the user's brain via some kind of "DataJack". It helps lift performance to a different level if you can have an entire HUD in your head and activate things with a thought.
So yeah, I maintain that a pilot sitting in a specialized chair, wearing a VR helmet and connected via neural link can look every bit the pilot that he is. The question is mainly a question of how to portray this the best, because I'm sure a decent artist can do it rather easily.