There are few problems I seen so far.
Geoscape is about web like game standing on points on interests and scanning them. While that's necessary doesn't need to be bad. There is a little problem. When you ally with a faction you lose 1/4 of scannable points. Then second faction you are left with 1/2, third faction 1/4.
Then there are some really bad decisions in game design. You are supposed to protect these small forts for story reasons, and to increase relations with faction... Thus fort protection is one of important mechanics. Considering forts are one of more important way how to get soldiers and supplies, theirs protection missions should be more detailed.
Problem 1. For some weird reasons you don't see ANY allied soldiers on defense mission.
Problem 2. You see all that numbers of enemy attackers and allied defenders... Yet when you enter the combat, you see instead of 3 enemies 7 enemies or worse.
Problem 3. There is no detail about damage caused by raid, or how long would take repair.
Then there is a problem with what exactly are Phoenix Point organization leftovers.
Are they?
1. Hobos/homeless equivalent in post apocalyptic world. (Few random/loosely related to project people found base and took it as theirs own?)Just small resources and people would throw them some weapons from pity, or to give them small support to find rest of Phoenix Project.
2. Equal footing, just smaller in numbers. Government tried to push for theirs funding before collapse and they survived collapse on one base.
3. Much more high tech group than the rest, but small in number. And they can't support rest of groups by technology, because rest of groups can't mass reproduce it.
This decision have consequences. 1. theirs research is based on reverse engineering and theirs own home research, because nobody wants to give technology to hobos.
2. shared research between ALL four factions.
3. mostly in house research but MASSIVE tech tree.
And now the more ugly part. The number of enemies per mission.
There are two ways how to make stuff like this. One way is to make few enemies and shoot at various body parts. Other is making horde of weaker enemies and weapons sufficiently strong to kill them on proper hit.
Phoenix Point did neither. As a consequence it feels like it's balanced to be winnable only with cheese.
Now let's looks at bad decisions they made.
Soldiers hired from factions come with body armor. Thus there is no need to produce one, thus well whole manufacturing process is nearly irrelevant.
Ammo and medikits can be manufactured instantly. ANYWHERE. As a consequence large part of game is basically simplified into pay and get stuff instantly. No item transport between bases, no need to delay fort defense because you need medkits.
Medkits basically allows to skip hours in infirmary. A simple pay to win scenario.
Damage and wound model has some flaws. For example, disabled head... Well it just need few seconds out of combat and it's fine. Perhaps soldier is a troll who regrow his head. Or his body.
Number of weapon types and research is definitely lacking.
And I seen weird stuff like aliens are using Phoenix Point weapons. Where did they got them? They are pretty unique. I didn't have loss before that, and the only way to get them is by manufacturing on Phoenix Point.
It's like they never tried imagine how in real world would Phoenix Point actually happen. What would be a consequence, and other stuff. If the game was 3 years in development, well that's weird because what I wrote is elementary stuff.