The game is very good and I like it. But why in the world would it FORCE you to sabotage allies or friends places.
It makes absolutely no sense that to increase your standing in a Faction, that you must destroy your other friends stuff. That is far from a common sense approach of doing everything you can to unite everyone to combat a common enemy.
Come’on Snapshot!
You can gain more reputation with each faction, giving then some special resources that you get via events, like giving then some old technology, protecting their havens, destroying pandoran bases, or attacking enemy faction havens.
And every faction hate each other, they have different ideologies and objectives toward the pandoran treat, this is way they support the idea of you destroying the other factions.
The factions what PP to work for them, not the other way around. They don’t unite with you, it is you who unites with them 
One doesn’t have to take the bait. Defend the havens and destroy Pandoran bases to up the relations with the factions. Then only do their special missions to trigger the next level.
And you have the special events which give bonus or negative rep with respective factions.
Thanks, I know how it works.
Still even just as bad, when you SAVE some earthlings from the evil invaders, 1 or 2 of the other factions dislike you for saving them.
This part of the game design goes against common sense and is poor implementation.
Destroy the pandoran base after a heaven defense and then you are mostly on even with the other factions and with a big boost to the one you saved.
Citadels are an exception, because they often give you only 10 rep to each faction like lairs instead of 15.
Probably a bug …
But overall I know what you mean. I personally also don’t like the big rep minus from other factions for defending heavens. Overall I understand why, but I would like it when it is a bit lower.
I agree in this point with @kokeaux
For me(!) It would be much more fun if you could unite the fractions and that they would join you in battle… imagine this: on a higher difficulty the game should become nearly impossible if you are not able to unite the fractions. But if you unite them you see everywhere in the world layer fractions troops attacking panda bases. And in this layer you could coordinate Strikes against panda structure with the fractions
(Edit: this could also mean that you could coordinate a heaven defence. So that you could defend NY heaven together with Anu, so that Anus Reputation should gain for NJ. This way you could manage the diplomacy between the fractions! And perhaps they will Help you defending a Base in the late game. The fractions could get allies over the time.)
And in the last Missions you fight side by side with all allies against the pandas…
Yes that is my “wet dream” of phoenix point. Unite all fractions and fight ONE fight against the pandas. Would be very satisfying in my opinion…
But i Think it will be only a dream… perhaps for PP2…
Perhaps for PP2. Narrative could be that we won battle in PP1, but war is still not resolved. So Pandorans after our major blow, managed to prepare second wave and new entities with even more deadly (just for the lore telling, not necessarily more deadly than they are currently in the game) creatures. Then in the course of inevitable doom we could try to unite the humanity, but that would need to be really hard task.
As for Phoenix Point 1 narrative is fine for me. Human population is unpredictable and it is reasonable for them to fight each other.
There are several things to be said about this:
Where I used to agree with you was Synedrion. I couldn’t get my head around the disconnect between their Anarcho-Syndicalist worldview and their hostile actions towards the other Human factions. Then I remembered how the Anarcho-Syndicalists behaved in pre-War Italy and the Weimar Republic (they spent more time fighting one another than the existential threat of the Fascists - at one point the Italian A-S’s even sabotaged the last desperate attempt to form a coalition against Mussolini, rather than co-operate with ‘Class Collaborators’), and I also recalled the less-than-glorious history of the only true democracy the world has ever seen. The Ancient Athenian Republic was so aggressively imperialist that it eventually forced its rivals in the Achaean and Aetolian Leagues to band together with the existential threat of the Persians to bring them down. Then, once the Athenians were out of the way, the Spartans and the Thebans turned on each another, until the even bigger existential threat of the Macedonians came along - by which time they had weakened one other so badly that not even the united front of Athens, Sparta and Thebes could stand against Phillip’s army.
So I’m afraid the history of our species suggests that we are more likely to team up with the Aliens in an effort to get rid of our ideological rivals than we are to unite against them.
That’s likely to change when the ODI gets replaced by a Human Population Counter (can’t find the Canny Link atmo, but it’s on Canny somewhere), but I suspect Snapshot will always want some way of thinning out the Pop to add tension to the endgame.
If it really bugs you that much, I suggest you look for Sheepy’s ‘Stop Faction Warfare’ Mod on Nexus, which lets you set a bunch of parameters and (I believe, though I’ve never used it) even turn the Faction Wars off completely.
Here’s the Canny link https://phoenixpoint.canny.io/feedback/p/replace-odi-with-survival-of-humanity
Thanks MC 
Yes you are correct Mich… I am also a history buff so I realize the tribulations of human history. However when faced to the greatest threat humanity has ever faced, the game would be more enjoyable if you united the factions instead of being penalized for saving people.
I agree, which is why I proposed the Path of the Peacemakers.
Sadly, it didn’t capture the imagination of enough players on these forums to recommend itself to the devs.