Some small and some big details but I think it' all important.
We should have the option to remove that noise (very annoying) that bips all the time when enemies are staring at us. Its important to be able to remove that alert icon completely or just the sound if we want to.
More coherence in the story elements. I'm not saying that the game needs to be super real but it need to be coherent! If a scientist is crouch and scary this should get attention from enemies soldiers when they see that!
Enemy's A.I. needs to be more tactical! Enemies should position better and get cover better.
Sell only one package! Stop ths thing of selling so different packages, dlc, season pass whatever.
Different presets, like arcade and simulator, not only difficulty levels. In sim mode the vehicles could have a more realistic controls, enemies could spot you from greater distances and skydive should not allow you to more forward for so great distances.
Helicopters controls should be like in Battlefield or Arma game series. There's no reason to change that model.
A multiplayer mode with more players, like 12 vs 12.