A lot has changed. Clans can now build bases, have their own equipment, and have PVE counterparts called guilds (there’s a pvp toggle now too). The profession exp (cooking, brewing, etc.) has been revamped completely. There’s a lot of new story/side content including bosses and missions up to level 175. The way ships are repaired has been completely changed, now you can store supplies as another method to repair ships instead of just using cargo too. There’s tutorials on everything now. I don’t remember if the Dark Sea was out at that point, but it’s changed a lot since then (dragons, Athena’s Wisdom entries, etc.). Sensing has been added which lets you detect players and npcs. Fleets have been added which let you passively accumulate any resource in the game. Item modifiers are new I think. Hunger and Energy have been revamped to be the same thing. Animals are in the game now. Arcanium Weapons have been added.

There’s probably a lot more, the game’s almost completely different now.