First, congratulations to the team for making such an awesome game. I've been playing since Xenonauts came to steam and have watched the game grow to what it is today, in addition to lurking on the forums. I liked several of the changes streamlining various aspects of the game (no more hassle of building individual rockets / clips, not having to grind through too many ufo missions for alien materials, air combat autoresolve, wraiths shooting immediately after teleporting, torpedos running out of fuel before hitting ufo's). I've enjoyed the game immensely since the latest release and just captured a ***spoiler*** praetor.
Having said that, I have some gripes.
1) The aliens seem to have omnipotent vision, always knowing where your guys are. While I understand that might be needed because the alternative would result in too dumb / too difficult to code AI, it does result in several rather unfair moments.
Case 1: My guys are unspotted, with the aliens on the other side of a hedgerow / high wall / trees. A grenade flies over and lands perfectly on someone's lap.
Case 2: Reapers wait behind LOS blockers and make a run for your guys only once they are in attack range. Other aliens camp and only come round the corner to open fire when close enough to deal good damage.
Case 3: Aliens reposition according to the closest soldiers, even those behind LOS blockers.
2) Another related point is that there is nothing a player can do against psionics. It feels cheap to have a Xenonaut randomly panic and go berserk and gun down his buddies near to him. Doesn't help that the morale bonus needs a proximity of 10 tiles.
3) As mentioned elsewhere, weapons feel too similar in terms of functionality across tiers. Sentinel armour providing 360 vision and Predator armour making strength a non-issue are examples of nice functionality additions to late game stuff.
4) Grenade throwing is a crap shoot. Soldiers often chuck the grenade directly into the prop right in front of them, with it landing directly on their toes. This probably can't be helped due to the engine I guess.
Other that the above I have no other major gripes. Hats off to Chris and the team. Congratulations on the apparent success the game has achieved. Thank you for your passion and dedication in creating this game, and all the best in your next project.