That's the one.

In 1994 the small studio Mythos Games led by Julian Gollop created UFO: Enemy Unknown (in America released as X-COM: UFO Defense). That game put together a highly tactical game in an alien invasion scenario. This blueprint was copied. One of the newer copies is made by Snapshot Games, led by none other than the same Julian Gollop who created the original. Phoenix Point is targeting to be the spiritual successor of the 25 years old game, modernized but keeping the central ideas. As such - like the original game - Phoenix Point creates some deep lore and engaging tactical gameplay with lots of options to decide the battle in your favor... or mess it up.

In the future the global warming releases an old virus from the permafrost, the Pandora virus. It's abilities include rearranging the DNA of infected life forms, leading to strong mutations. It even mixes up DNA from different creatures to create something new with abilities and traits borrowed from these different creatures. The mutated creatures start to attack the human civilization, leading to our downfall and near extinction.

In this peril an old organization get's reactivated, the Phoenix Project. Sadly it happens late and most of human civilization is broken. The surviving humans gather in Havens, which are mostly aligned to one of three factions. These factions have different standings on how to deal with the changed world. While the disciples of Anu, a new religion try to incorporate mutations to develop humanity, another faction named New Jericho tries to exterminate the virus and the mutations. Synedrion tries to advance human civilization and is discussing how and if they want to use the Pandora virus.

You get control of the Phoenix Project and try to deal with the mutated horros, protecting the remaining survivors of humanity and dealing with these factions.

https://www.youtube.com/watch?v=06rGDSXK9fE&ab_channel=PrimeMatter

More hints:

#38: Help the kingdom of Nostria.
Play either as Elisa, Aivar or Katharine.
These are the Paladin, Fighter and Magician of the game (in that order).
This game is part of an old series of tactics games, but although many games preceded it, it just has the number 2.
In the beginning your character is thrown into jail because of... the king dying in the moment you get in the spotlight.

#37: Guessed by coolbeans: Pillars of Eternity

#36: Guessed by S.Peelman: Resident Evil: Revelations

#35: Guessed by UnderwaterFunktown: Starcraft

#34: Play as Humans, Ancients or Ardyn (or later as Gwdir or Tomek)
Catch Cats, Lopen, Rabbits, Snoots, Squeaken or Chicken.

_{ranking in the guessing game, list so far}

Well guess we'll some more hints for these ones:

40) Perhaps one of the most famous cases of a "bug" becoming a feature
Hint 2: And a vital part of competetive play

39) This highly acclaimed title was caught in some controversy this year
Hint 2: I belive the arguments were "It's unwarranted", "It's too expensive" or "Take my money!"

38) As below, so above
Hint 2: For the first time in this series the protagonist isn't silent

37) The revival of revivals
Hint 2: Since this remake that started a trend came very long after the previous remake for the series

36) Most characters from the original game return in this sequel, though you only meet a few of them before the post game
Hint 2: One of these characters, the one you interact with the most of the returning ones, is the "final boss", though he didn't have that role in the first one

#40: Cancel in Street Fighter II?

I was thinking 40 would be about juggling with the first hint, but I wasn't sure. That would make this Street Fighter II I think. 38 sounds really familiar too, but I can't place it.

Second set of hints then.

#35

-"What began as a conflict over the transfer of consciousness from flesh to machines, escalated into a war which has decimated a million worlds."

-"The Core and the Arm have all but exhausted the resources of a galaxy in their struggle for domination."

#34

-Heavily inspired by a series known for its relaxing nature (Stardew Valley)

#33

-Betrayed by one she loves, the girl seeks vengeance, and embraces her role as the Lord of Calamity (Tales of Berseria)

#32

-Picking up one year after the events of the previous game, the empire has annexed another region during that time, and you find yourself heading a new class of military students (The Legend of Heroes: Trails of Cold Steel III)

#31

-Lust for revenge rarely ends well, for anyone involved

-You get to witness both sides of the story, though some people weren't happy they were "forced" to play the other side

Is #39 The Last of Us?

Is #37 Resident Evil 2?

#31: The Last of Us II?

Nope, it's not Street Figther II, though this much later game does have some things in common with it.

Both correct! And with RE2 it's of course specifically the remake as the hint suggests.