Just downloaded the demo and there are definitely issues with the cover system.
The cover penalty is applied, or at least displayed as applied, irrespective of what side of the cover you are on. That means hiding behind cover inccurs an accuracy penalty from the cover you are hiding behind.
How cover impacts LOS seems "unrealistic". Shooting at a standing alien through a medium obstacle has a 30% chance of being blocked. Have your LOS clip a three pixel corner of a large obstacle and your shot has a 50% chance of being blocked. It's easier to hit an alien through three blocks of shoulder high raised terrain than it is to hit an alien who's elbow is in cover.
There needs to a two block area around the xenonaut where cover does not affect LOS. Also the chance of a piece of terrain to block LOS should be worked out on how many LOS pixels cross through the terrain not a flat rate.
