The tech tree has some issues. For a lot of it there's many ways to progress, or there's many ways to get the core techs that let you progress. But some stuff like captive bugeye or the shadow lamp* can just never show up and keep you from unlock large and important branches of the tech tree for more than a year. It's especially an issue for all the various story missions, where bad rng can keep you from a tech for a few months, then bad rng can keep a mission from spawning for a few months, and then when you finally do go the design of the mission is ruined by the fact that you've progressed enough in tech to trivialize the enemies. It's also kinda frustrating when your story progress just stops for more than a dozen game hours and there's nothing you can do about it.
The variety in mission and gear restrictions can be pretty cool, but it can also feel a bit sadistic at times. You'll just not be allowed to bring any good armor, or vehicles, or strong troop types, but the enemies will still use their normal high tier troops (I guess their carapace armor is just naturally vacuum rated, while my power armor isn't).
Spoiler:
The strong enemy factions also tend to have spotter/sniper on every unit, which removes all consideration of smoke, light, camo, invis and sanity from the equation. You either kill everything in one turn, or you make sure there's a solid wall between all of your troops and the rest of the map, because the alternative is every enemy on the map shooting at you, even though it was 2 turns since anything saw you. You learn to take all missions in daylight, just because at least then everyone sees everything all the time.
The biggest "to be continued" kick in the balls was the technocracy line for me. The palace mission is cool (at least the first 2 parts, the final one is shit), but then the reward is -3k score for killing govt troops and a "lul, the princess is in another TBD castle". And so it feels like a huge waste of time and effort. The champion gudrun story also felt a bit like this, but at least that one rewarded some cool weapons, even if it ultimately went nowhere. I'm also a bit upset I got an unfinished red mage line due to my choice of gudrun, with absolutely 0 justification for why.
The shadowrealms are really cool in theory, but the balance is completely out of whack. The necropolis mission is one of the hardest in the game, but isn't actually more rewarding than the 2nd fear land mission, which has like a third as many enemies and no strong ones. I had the gray spellbook, so I didn't have much issues with nightosphere land, but I imagine it to be pure torture for every other codex. Huge map with low visibility and flying enemies who like to fly so high you need to stand almost exactly under them to spot, and super limited ammo and weapon counts. But also, the first shadowlands mission with the fear prisons is really easy and I was never in danger of even landing someone in sickbay for a long time, let alone die.
Midgame armor choices all felt bad to me. Just piles of odious tradeoffs (no inventory, no running, crippling weaknesses, crippling freshness drain...) for marginal gains in other areas. I went straight from plate and gravboots to assault and blitz. I think I also accidentally broke the intended research progress speed at some point (80 brainers was just too much apparently), as I just ran out of meaningful techs in the middle of the third year, and the whole 4th year my brainers spent 90% of the time idling while waiting for more rare captives to come in.
The gnomedisc (and therefore also the hovertank) was a lot of fun, but all the non flying vehicles felt kinda shit by comparison. Not sure why you'd field a XEC over a hovertank.
The cost to build the final transport and reach cydonia is kinda ridiculous. There's an alternate way (titor), but it's just as bad if not worse. 12500 hellerium and 142 engineer years is just 10 times more than it needed to be. The craft requirements for all the different mission types can also get a bit crazy: When you need a 1 seater, a <6 seater, a <13 seater, ipl, sub, mun and primitive it starts to feel very ridiculous, even if you can combine some of those categories.
I'm a bit annoyed that factions stop using faction specific weaponry for some missions. Mercs doing base assaults with plasma isn't the worst thing, but spartans wielding heavy plasma is stupid.
* I still have no idea how you're supposed to get this. I wound up hacking it in to my save, because the ufo it spawns on just refused to appear. And during like the 4th year, when they did start spawning in decent numbers (because of stuff locked behind already having it), I couldn't manage to not explode them even when using the weakest craft weapons I still had. I could have used
I suppose, but when you're considering using endgame tech to unlock a mission that wouldn't even be particularly challenging 12 months in there's something seriously wrong.