I love manual flight. Gimballed thrusters are cool. I don't love using my mains against my will.
We can toggle fly-by-wire off in the tuning menu. I think it would be cool to also be able to toggle off the autopilot/fly-by-wire's ability to fire main engines, at the very least when pressing the 'manual forward RCS' key. This is the literal only reason I switch off fly by wire.
Also, while the above is the main suggestion, on a similar note it might be nice to toggle the 'stop rotation when translating' function of the fly-by-wire as well. For pilots who are used to zero-gee hand-flying, it feels more natural to use that rotation to our benefit, or cancel it out ourselves. Tapping the stick and suddenly halting my turn unexpectedly is a bit unnerving, and in my mind, just an extra thing I have to do to get spinning again (when fly by wire is intended to REDUCE workload for a pilot).
(At this point, a simple 'fly by wire but only gimbal my thrusters' is what I'd be most happy with..)