The game is not done, sure. But it's still pretty playable in its current state. However, there are several things that positively make me cringe and/or grind my teeth on a regular basis. Here they are, grouped by gameplay area:
First, the more benign and easily fixable stuff:
Graphics And Interface
Trigger-happy right clicks. Opening a grenade menu takes several attempts, fine. But opening/closing a door suddenly eats all your AP.
Why can't I see the state of my aircraft in a table without spending 5 minutes selecting a UFO and pressing 'Intercept'?
Two words: Invisible enemies. And stuff hidden behind a wall that's next to impossible to target.
Next, the stuff that is most likely to get fixed, as it's by no means finalized. Also, some stuff that, sadly, won't get fixed, as far as I understand:
Pregenerated maps. Effectively removing 50% of replayability, and trekking over the same terrain, unsurprisingly, gets really dull after a while. Also, one of the farm maps has a 'void hole' that is rather puzzling to see.
Bloody. Impassable. Solid. Massive. Hedges. Everywhere on the farm maps. Would be nice to have a flamethrower and burn them to the ground. Go have a look at a real farm.
Researching '#####' to be able to produce '#####'. Placeholder texts, anyone? Other things have them, e.g. 'alienbase.sebilian.medium' or somesuch.
No viable production-based economical strategy. Stuff you produce has exorbitant production costs, and sells at ridiculously low prices. The only option is to do as many missions as possible. On repeating maps. Ugh.
Automated Research/Production. This is a controversial one, but I have fond memories of having to build alien containment (containment escape missions, anyone?), manage the stockpiles, build ammo and juggle dozens of research projects.
Lore inconsistency. First, we have radio-based telepathy, then genuine psionics? If their telepathy is radio-based and we have decoded the language, wouldn't it make immediate sense to produce field/global radio detectors to track units in combat and decipher UFO targets and intentions.
No psi/advanced training??? Actually, no training, period.
Nine shots per magazine. To be consistent with the chosen upgrade mechanics (upgrade by magic), it would make sense to have some technologies affect the ammo capacities of weapons.
Combat. I intentionally omit all the bugs.
Lack of strafing. Limited mobility options in general.
Why the hell is the UFO in combat a selectable object? I had a really bad time trying to target an alien who was sitting in the open right next to it, because the cursor jumped to the Battleship itself. I had to send a soldier to open the front door to turn the UFO to it's 'blueprint on the ground' state before I could target him.
Useless stun gas.
Missing grenade effect areas.
Hidden movement mechanics. The camera is not exactly helpful there.
Teleporting and shooting wraiths.
Enemy/Civilian AI in general.