While making a mod of mine, I've encountered some "difficulties" regarding the interaction of engine flares with ships' and deco weapons' sprites. The biggest one - the lack of an option to force the engine flare to be rendered "under" the ship's sprite, making the use of deco weapons mandatory in the case when I want the engine to be partially covered by other parts of the ship (wings, armour plates etc.).
A rather "simple" (as I do not know how exactly difficult it'd be to implement into the game engine) option to decide whether the flare should be rendered on top of the sprite or under it would be a really nice addition and a saving grace for more "complex" ship designs for the modding community.