2 things were reengineered for cooldown with AE:
1. Rather than use the CooldownReduction ability in skill modifiers like Lay Trap, they used the Modifiers/Cooldown Time ability. For example in Lay Trap pre-AE the value was:
skillCooldownReduction,18.000000;27.000000;36.000000;44.000000;52.000000;60.000000;66.000000;72.000000;78.000000;85.000000;92.000000;99.000000,
In AE it's: skillCoolDownTime, -1.000000;-2.000000;-3.000000;-4.000000;-5.000000;-6.000000;-7.000000;-8.000000;-9.000000;-10.000000;-11.000000;-12.000000
2. In XPack/Game/gameengine.dbr the All Groups/Player Info/playerCooldownReductionCap was set to 80 instead of 100.
So yeah, the cap was set to 80% max, but the new way of modifying cooldown with negative values also affects cooldown reduction as you don't stack %s