A few of the initial things I've noticed are:
All the maps have been redone. The areas look and feel like they were overall designed better.
The mining areas are in towns now and instead of mining individual ore deposits, you just go in and mine (the mining area used to be like 4-5 maps to the right of Elgaill). However, one pick axe used to last you forever and now you have to buy one for each use.
Cooking is much better now. The pots restore more than shop pots (before they were pretty much the same restorative value) and the recipes are different.
You don't have to be level 20 to use the storage any more.
A lot of the quests are different (I don't remember there being any timed quests outside of instances as well as ones you have to avoid being hit a certain number of times), as well as new mobs.
Dagger type thieves now attack 3 times instead of 2 with their normal attack.
The skills they have now at 1st job are completley different and superior to the old ones. That might be true for all jobs though but I'm not sure.
The changes may or may not have been universal, but the way it is now is definitely better.
And my apologies for the long, slightly offtopic post.