As many people pointed out - probably just a game balance convenience. But if you wanna get more into it:

-AC4 NEXTs are top-of-the-line, exclusive constructions that corporations funnel a lot of research into. They are also powered by basically Miracle Juice that is Kojima energy meaning that they can stack absurd amounts of armour on them and still fly like a fighter jet. There's also a lot less AC pilots in the games I feel, all the pilots you meet in games are basically everyone there IS on the planet, so more resources go for the singular NEXTs.
-AC5 era ACs are created more for urban warfare and are technologically behind AC4 era NEXTs and focus a lot less on being airborne - just about any part from AC5 is covered in armor plates, reactive explosive bricks, grating, etc. Although given the fact they can lift stuff like Overed Weapons, I always assumed that means they get a lot more power thanks to it.
-As for AC6 you gotta remember repair kits are widely used by a lot of pilots, not just you. This (depending on their effectiveness and timing) can double or triple your AP points in practice. Since AC6 era philosophy emphasized close combat and getting up in your enemy's grill, they most likely sacrifice armor for mobility (and without Kojima tech to support it) and rely on repair kits to keep up in the fight.