Thanks for the suggestion.
I'll see what I can do about implementing a raycast system in order to better determine what the player is precisely aiming at.
However, I will not be deviating from the isometric perspective as this again was explicitly designed to invoke the orientation and gameplay style of the original Zaxxon. I will also be keeping the Y-inversion controls as this is both an accurate invocation of Zaxxon, and an authentic representation of aircraft pitch controls. It may take some getting used to, but it's easily manageable, once you get the hang of it.