there's no good solution since they created this problem themselves.
The fact that you have to gear up useless pilots is annoying in itself, but with pilotless ships you make the earlier pilot investments totally irrelevant if they are on par or better than piloted ships (fortunately or not, point of view, pilotless ships are not better).
Also some ships have not one but 2 or even 3 pilots so that's one more headache. I think they should either add pilots to pilotless ships or remove the whole pilot system altogether.