There are many scenarios with three or more factions that currently we can't really do. Syria, for example, had the Assad government, the rebels, the Kurds, the Turks, the Americans, and the Russians, and while some of these worked together to varying degrees, reducing them to two coalitions removes a lot of nuance from the situation.
I'd love to see three (or more) combat factions, and the ability to set each one as allied / neutral / hostile to each other faction. I.e., Green is Neutral with Blue, and Hostile with Red. Ideally, also the ability to change those alliance settings with a trigger mid-mission.
Imagine being able to make missions where the American air defense doesn't attack you on sight, but does create a no-go-zone. Where you fly an Israeli strike against an Iranian ship heading for the Suez canal, and Egyptian air defenses are shooting at both you and the Iranian escorts. The possibilities are endless.
