One of the biggest features I'd like to see implemented is a hit location based damage system with targeted locations on the humanoid form (Head, F/B Torso, L/R Arm, L/R Leg) and location for non humanoid / mechanical targets.
Armor could then be designed to cover specific parts of the body allowing for the balance of weight vs coverage.
Body parts would have different hit points with varying wound severity (Slight, Moderate, Heavy, Incapacitated, Destroyed)
Wound effects based on location and severity (i.e An arm wound could result in x% loss of accuracy all the way to being unable to handle a two handed weapon)
Players could target specific areas with varying hit modifiers
Allows for greater range of alien/vehicle strengths and weaknesses
This along with basic cover and concealment would make a very nice, sleek and easy to understand damage system.