I doubt there will be any more balancing changes. I agree that friendly fire is a problem in this game. You have to be careful that none of your soldiers are near the line of fire of other soldiers.

I haven't noticed the accuracy problem you mentioned. The percentage to hit the game gives seems to be accurate when I play. The only exception I found was throwing grenades from high ground to low ground. And grenades in general are less accurate than I think they should be.

I have not noticed Alien ships types becoming more powerful, except that each new type is more powerful than the last. Be sure to keep upgrading your interceptor technology - both the types of interceptors and the weapons they carry. When I play I make researching interceptor types and interceptor weapons my highest priority. Two aircraft carrying torpedoes should be able to take out anything except for the biggest ships, but even then would only need a few shots from guns to finish them off.