It's terrible how XCOM has now set the standard with what it possibly the dumbest cover system I've seen. Even the 1994 game had a more nuanced cover/los. XCOM technically doesn't even have a cover system because "cover" merely reduces to-hit chance, it doesn't provide actual cover, it doesn't block shots. Not to mention the game's derpy physics and line of sight.
Xenonauts' cover and line of sight/fire are not nearly as fluid and precise as in JA2 but at least this game makes an effort to do it right.