I think the biggest thing contributing to the lack of atmosphere is that the world simply doesn't feel finished. There's massive lack of points of interest, and even those that are there are just...props. Like those 2-d scenery backdrops used in B-movies. Go to any of the hamlets. They all have about 6-8 NPCs with small snippets of dialogue and NOTHING else. Plenty of them mention goods that that town makes, but I've yet to find a single store at any of them. A few buildings, but none of them can be entered. Docks that serve no purpose. Not a sub-quest in sight.

You see this in other places as well. I've did a little bit of exploring, and for the most part, there's simply nothing to really explore in the game. What little can be found is simply placeholders for future stuff - NPCs guarding areas you can't access yet and similar.

People complain about this and that about the game, but the real problem is that it was released WAY before it was ready, and SE was arrogant enough to think that the media would simply give them a pass on selling customers an unfinished game. So now, they're trying to play catchup while at the same time doing a 180 in terms of PR so that they can try to regain customer confidence after their blunder.