Personally, i do not think that keeping or removing these would make that much difference in terms of gameplay: most of these IFFs are gone with the Guard systems and sticking to that obsolete concept is not necessary.
For convenience's sake - let go of them with appropriate changes applied where it is necessary. Maybe, exclude the Coalition from this since it makes more sense for them to have separate IFFs.
Peace, being the distant dream it is, comes inevitably, and goes hand in hand with justice.
Cursed be the war. Heroes never die! @Vitoniz30 @Connor