1. Soldiers permadeath
from what I've read and found out it will be difficult for your soldiers to die permanently, they are more likely to pick up a negative trait like lose of limb, or drug addiction.
i like this because it will take away some of the frustration of leveling up a soldier and then getting killed. But I feel like this needs to balance out some. If it turns in to an alien attack is always knocks your soldiers unconscious never killing outright I feel like that will take away some tension in the game. Oh it's fine if I leave my soldier in the open they just have to heal at base latter.
2. Aliens changing in size
the alien mutation system sound really cool but one thing that raises some concern for me is that they can change size. It really just matters how much. If a crabman becomes bigger than a crab queen I don't think that would be fun. Oh look no one humanoid sized enemies everyone is a giant.