I remember reading somewhere here that the reaction fire system as it stands is crude, unfinished and planned for overhaul, so I think it's not worth complaining before it's remade.
However, it doesn't look to me like your soldiers are really meant to shoot aliens as soon as they pop into your LoS. Aliens should spend enough TU's (enough to react, aim and shoot) in front of a soldier doing something before he can do anything about them, this is how it's meant to work I think.