Unsure.
In JC4, the AoC faction was present in the final battle and it required a lot of setup to weaken the area first. So that one made the most sense in a sort of story-telling way.
The one in JC1 was the most difficult, because of the number of times the player is likely to get killed in the extra long battles in the mission. Rico has to alone fight against like 1000 enemies and maintain maximum heat while on foot in an open ground area for a number of minutes.
In JC2, the stakes were the highest with having to fight the enemy boss and disable nuclear missiles mid-flight in order to avoid a global nuclear war. But on higher game difficulty levels the hacking is extremely difficult. (Maybe it's easy on consoles, but not on PC.) There's actually a mod that makes the hacking easy. The enemy base interior is also quite creative.
JC3 has the only plain generic boss battle where the player just has to improvise to either drop something heavy on the boss, or get good with the grappler.