Options like these crank up the heat inside the alien-infested pressure cooker that is XCOM by rewarding smart play and punishing mistakes. Other players I know swear by Aiming Angles (bonus accuracy if you're near flanking) and Red Fog (accuracy penalty if you're injured) and won't play without them. This may sound like a minor detail, but in a game where a few percentage points are the difference between brave and grave, messing with stats like this can really surprise you. But in party-time-second-wave XCOM, you can enable Not Created Equal and Hidden Potential to mix up your rookie's starting stats and how those stats change between levels. In boring-old-regular XCOM, rookies are basically all carbon copies of each other, with identical stats and level progression.
My personal favorites change how your soldiers grow.