It's definitely a cool idea.
I've been playing with a manual aim toggle for a bit. Basically just turns off/on the FCS if you hold the "lock-on" button, and it works okay. Everything being projectile-based (except lasers) makes it take some getting used to. Just needs to take the player's camera settings into account more since at higher speeds, the offset between the player (the origin of the projectile) and the camera (origin of the aim point) can get really large so shot trajectories can get really wonky.
Maybe an additional function like VD where it automatically toggles to a cockpit view when you turn off the FCS would be useful. Basically minimize the offset between view and shot origins. An optional zoom function would be slick as well.
Personally don't know about making weapons that absolutely require manual aim. Maybe hitscan weapons? They're definitely harder to balance alongside the auto-targeting.