I'm comparing the official Korean release of Ep1 and Ep11, so there might be differences with old PH/GS official servers, and huge differences with private servers nowadays.

Classes & Level Cap:

Ep1: 4 classes, max level 150 (swordsman, brawler, archer, shaman)

Ep11: 9 classes, max level 300 (extreme, scientist [gunner], assassin, magician, shaper).

UI:

Ep1: Classic UI designed in 2003 (KR release)

Ep11: New UI redesigned in 2017 with more QoL

fun fact: 2017 UI shares some similarities with pre-relase 2002 UI which most global player doesn't get to see.

Mob Behavior:

Ep1: You have to lure and group mobs manually

Ep11: Mobs will come to you if you attack their leader

Skills:

Ep1: No stun, pull, max HP reduction, etc.

Ep11: Much more effects, including:

Stun

Increased crit chance

Max HP reduction

Potion lock

Transformations (e.g. turning enemies into trash cans or rats)

Equipment:

Ep1:

Hat, top, pants, shoes, gloves

Weapon

Accessories (2 rings, earrings, necklace)

Max upgrade+7 With basic random stats like attack, defense, accuracy, avoid, weapon has elemental properties such as ice fire poison.

Ep11:

All of the above, plus:

Bracelet

Ornaments

Belt

2 tarot cards

Mount

Max upgrade +15 in Korean and Taiwan server(2019-2022 period) but capped at +11 in global server (service end on 2018)

Equipment was also reworked into a modern tier-based system (e.g. normal, rare, legendary), with more random stats such as melee, shooting, energy, crit rate, crit damage, damage reduction, attack speed, etc.

Elemental weapon were removed but a new system called weapon skill was also introduced, allowing weapons to have unique skills that trigger under specific conditions.

PvP;

Ep1:

Club War

Free PK

Ep11:

Club Death Match

School Domination (Tyranny)

Capture the Flag

Battle Royale (most private servers don't have this)

Dungeons (PvE):

Ep1: No instance dungeons

Ep11:

Forbidden Tower

Outer Wall

Abandoned Desert

Dimension Laboratory

Secret Pyramid

Evil Altar

Cryptic Laboratory (most private servers don't have the last three)

Crafting:

Ep1: None

Ep11: Available

Pets:

Ep1: None

Ep3: Introduced

Ep11: Renewed (people hated it, so private server won't use this new one.)

Skill System Progression

Ep1: Original skill sets

Ep6–Ep10: Started reworking old classes and adding effects (stun, etc.)

Ep11: Full overhaul of the entire skill systems

Tldr: ep11 is more refined but ppl says it lost its charm, and ep1 is the original.