Well, good work, seriously, buuuuut:
Pulse weapons too strong
The research is extremely complicated and there is very little ingame clues, Towards the endgame it is complete mess, ingame hints and keeping tracks of what you need would be appreciated a lot, especially the need for dreadnought, boy was I glad I could finally end it.... (golden rule is stun everything and pray).
U stunned it.. gratz / loved it but the lore is REALLY needed, keeping fingers crossed ;). The lore, where written is way off the "truth".But yeah, I know you know :).
Nerf pulse, way too strong.
Anti-matter rifle MK2 too strong / too early (might have gotte lucky dunno)
Nerf blood weapons ... way too strong.
Nerf reapers... way too strong, armor should at least give you a fighting chance / like gave probability to resist or so (as it is best thing is to just wait and get them with reaction fire).
Nerf stun gas towards xenonauts, way to strong and stupid that armor does not counter it.
AI for the "civilian" soldiers could fight more and hide less... but I understand this is not a priority :).
The aircraft weaponry has quite a lot of useless stuff, should be balanced more I suppose (mag cannons and the second graviton torpedoes does it until the very end, phase 4 weapons are quite disappointing).
The aerial combat is way too hard without the easy mod and is too tiring. doing 4 - 6 manual almost an hour long combats every wave will burn out everyone (when it is from time to time it is great though, please diverse the ufos more). Some ufos like terror dreadnoughts turn rate is rather extreme. Ufos speed is ridiculous, big are too slow, small are too fast, does not really make sense. I like the old xcom model better (good try though).
Base defense missions too easy, I liked the frequency, that was quite on point.
Shock grenades can detonate ANY explosive - I liked it a lot, makes kinda sense too. But rocket launcher is pretty much useless this way.
Gimme psionics and researches for different praetors, come on, you can make it. Implement some OP very endgame stuff, we deserve it after hundred of hours of grind ;).
Timberwolf can be assigned spiritwolf weapons and becomes tank.... not sure if it works viceversa.
Once you are superb all over the world it becomes almost impossible to lose them if if I neglect the globe for a year... perhaps the increments and decrements could be looked into.
I loved the reward for terror missions, feels really good. Perhaps you could lower it a bit though.
I love how you can nurture your alien fortress, it is kinda pity that the race is randomly chosen at the beginning (can save/load it), would make sense if it would get the race for good from the ship that established the base.
Would be great if ufos could be shot down by the nations, you should work further on the idea of "Xcom" joining the fight not being the only force. (percentage based, not the capital ships I guess...).
Production of items should make money... or perhaps giving plus points towards the rating from the nations... make sense, balance required ;).
Some sort of verbal rating could be implemented like in the old ufos, would feel good.
New soldiers should have better stats and should vary A LOT more (40-80), a lot, could progress with the phase. It does not make sense that your guys can get twice the fast as "the best" spec ops. In fact they should not get that much improvement at all I believe. If injuries could lower their performance that would be good. Forcing player to rotate more soldiers would be good (make recovery twice, triple longer!), instead of just kill/load/swear replace.
U basically lowered the amount of soldiers and "forced" player to use vehicles... not cool, like vehicles are super needed anyway but the old ufo's "let the player decide" is better. I want to bring two mechs! (perhaps not right into chinook but....) Repairing of the vehicles could be nice idea, but might not be worth the hassle.
That's all I can think of I suppose. I understand it is a lot, and hard/impossible to do, just my thought ;).
All in all - totally awesome job you guys, it shows it is not finished but it stole another week of my life :D, and here I though im too old for this kind of hardcore gaming :).