Hi i was able to play a bit of this mod! The modeling and particles are great! I really like drop pod and mother ship landing animation!
I noticed the problems of assualt tripod missing its target, which is caused by your particle projectile going too fast. Its speed is set to 50 but Glest can only accurately detect collisions of particles going 25 or less. It may seem like a feature but weather or not it hits or not is not a random occurrence if assault tripod shoots a (non moving) alien and it misses its first shot it will always miss the alien. As for chemical trooper missing if an enemy is in front of him i believe its caused by the particle starting at -1 (or 1 dont remember) as a general rule x and z should not be whole numbers (eg 1, -1) this causes a bug where the "bullet" fires straight up or straight down (depending on attackers height vs defenders height) and since bullet spawns on same square as defending unit a collision is not detected. It seems fine to have y values of any value. Hope this helps. When i played it took me longer to have infantry than assault tripods, maybe you could limit to only infantry in the beginning?
As for the issue of turret maybe there could be two modes: Max shield Weak attack or Max attack and Weak shield. Or to have different shield types strong certain kinds of attack, but be weak vs other types, eg strong vs air weak vs land or strong vs plasma weak vs ion. I don't understand the point in building a foundation then upgrading it to turret, you should just build the turret from the start.
Keep up the good work!