Maybe I’ve missed something important, but from what I can tell area targeting with a cube always covers a larger area compared to a cone at the same disadvantage level. On top of that, a cone must originate from your square, while a cube doesn’t have this restriction. It seems like a cone is just the worst option in every situation, except the rare cases where you actually want to target a smaller area.
||Squares Targeted Cube
||Squares Targeted Cone
This effect gets worst as the size increases, or if you consider the area in three dimensions instead of just two. As the size of your area effect increases, cones become half as effective as cubes.
Should something be changed to encourage a meaningful decision between the two? The most obvious fix to me would be to make the disadvantage penalty for cones one less than the size of the cone. This would give cones a slight advantage at size 1 and 2, and make them more equal in area coverage at sizes up to 5, when compared to a cube with the same disadvantage penalty. I think this would be a fair change considering that cones also require proximity, but someone with more experience with the system might see it differently.