Three ideas:
-a bit more AI added to ships. If they notice a bomb/torpedo attack they could do some evasive manouvres, instead of staying on the path planned in Mission Builder. Like here:
http://users.swing.be/navbat/edito/navires/yamato2.jpg
-plane damage modeling effect not in IL2: in some planes when getting enough damage, the landing gear would go to landing position while flying and slow down the plane
-add a small explosion object to mission builder. Person making a mission could place such object inside buildings, static ships, fuel trucks etc. When it is hit during game, it would produce an explosion. The strength could be set in mission builder.
This way you could simulate things like ground attack hitting an ammo dump, fuel truck etc. Player couldn't see this effect in advance, because the object would be hidden inside bigger objects.