I think it's safe to say that everything you see or do in the game has been changed in some way or other. You probably wouldn't recognize it as the same game.
I recommend skipping Build 13 and getting the latest Build 14 when Pieter updates it this weekend. It should be fairly stable (probably no worse than Build 13 Final) by now, and although there are still some things missing the game is solid. Build 14 adds too much good stuff to the game, and I couldn't go back to Build 13 after playing it.
Gameplay changes, new quests, whole new quest lines where you play a different character (you can be Horatio Hornblower, for example), new islands on the map, new characters, an entirely new interface, better sailing and ship combat, reasonable weather, almost all the graphics have been changed and improved, the list goes on.
Edit to add: If you enjoy sailing you can sail between islands without ever using the worldmap. There's an optional new skilling system that assigns skill points as you do things that would increase that skill, rather than assigning them manually. You can visit the deck of your ship and move between the hold, crew quarters and deck in a natural manner.
The game includes a huge variety of ships now. Some new weapons have been added. You don't have to stop playing when you complete the last quest, or you can ignore the quest entirely. There's an option to ignore Malcolm during the tutorial and just leave, ending up on some random shore without much of anything to help you, called Stormy Start.
The towns are populated with a variety of people you can talk to, get your pocket picked or pick someone else's pocket. Wandering merchants can have some very good stuff available.
Goods are priced high enough that buying and selling cargo makes reasonable money. You can be a trader or a privateer, as you wish. The governor will give you quests to sink specific ships. You can buy treasure maps and hunt for buried treasure, which may or may not be there. <img src="style_emoticons/<#EMO_DIR#>/smile.gif" style="vertical-align:middle" emoid="

" border="0" alt="smile.gif" /> Lots of piratey stuff to do.
Welcome to the forum and enjoy the new game. <img src="style_emoticons/<#EMO_DIR#>/smile.gif" style="vertical-align:middle" emoid="

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Hook