The biggest difference right now is how hit detection and "flinching" is handled. On AEGIS what's supposed to happen, is server detects a hit, tells the client it's hit. When you're hit, you do the flinch animation, and at that point you resume walking. If you were less than halfway through a cell when getting hit, then you get moved back to the start of the cell, otherwise you continue going forward. At the end of it all you still keep on moving though. What endure is supposed to do is remove the flinch animation. There's still the half-cell check, so it's still possible to hitlock monsters/players with endure (just attack faster than their walk speed and they'll never move more than a half cell before getting hit). That's how on officials high ASPD snipers would hitlock slow monsters like Atroce or Ktullanux.
Athena currently does none of this. When you're hit your movement actually stops and resets. That's why you rubberband like crazy when getting hit, because on the server you've stopped moving but your client thinks it should still be (because on AEGIS that's what's supposed to happen). Endure removes all movement hindrance, when you get hit you just keep on moving uninterrupted, so endure is actually better on Athena.
As far as mob AI goes, the easiest way to explain is that each monster is a state engine. They all have a state they're in, and when a condition is checked (IE I got hit or a target came within my visual etc), it changes into a state like ATTACK or CHASE or stuff like that. On Athena, target is an attribute. When you walk out of sight range, target is reset and the monster returns back to idle since it has no target. On AEGIS, targetting is actually an active state, so when you leave sight, the monster still actually has you as a target. So for example, if you hit a normally non-aggressive monster, walking out of vision doesn't immediately reset the aggressive state. A monster will hold aggro until it's lost target on you long enough to time out the aggressive state. On Athena once it's lost target the aggressive state is considered invalid and the monster goes back to passive. This is just one of several divergences between AEGIS and Athena mob AI.
I actually just pinned down official Cloaking behavior and how the speed boost check is handled. It's been wrong this entire time. When you're on a wall you're supposed to move faster than off wall. Originally this check was done on every cell, once you left a wall you lost your speed boost immediately. This is not how it's handled on AEGIS. On AEGIS the check for speed boost only occurs on the cell your walk ORIGINATES from. For example, say you have 2 walls, and a gap about 10 cells across. If you start from one wall, and click on the opposite wall, and do not give another move command, you'll actually keep the speed boost the entire time, despite crossing a gap without touching any walls. But, if say halfway through the crossing you give another move command, you will immediately lose the speed boost, because when you give that second move command server checks your position and sees you're not on a wall and takes away the speed boost. The wall check for if you remain cloaked happens on every cell regardless, so if you're using cloaking levels 1 or 2 and you cross a gap you will still lose cloak immediately.
There's a lot of older skills like that that have been wrong that nobody's actually bothered to get the proper behavior on that can make drastic gameplay differences.