For realism, the ultimate thing that's missing is the game uninstalling itself and preventing you from reinstalling it the first time that you get killed or shot down over enemy territory in the game.
The second most important thing that's missing is an interface that causes the player to experience mild to moderate pain when you pull extreme g's, or causes you moderate to severe pain when your pilot, or any member of your crew, is wounded.
More seriously, the main problems with IL2 are:
1) lack of dynamic center of gravity
2) lack of realistic fuel/oil management
3) limited human performance factors (e.g., detailed pilot/crew skill levels, crew/pilot morale, fatigue & group tactics, oxygen management at high altitudes).
4) Unrealistically aggressive AI.
5) Lack of dynamic weather.