When I've already been into the dungeon and done everything there is to do in there, I noticed no impact anywhere. Nobody said anything. No progress in any of my quests. Then I was notified by an NPC that I could get into the dungeon another way; perhaps something would happen then? Nope, nothing happened. So what's the dungeon there for?
I even got to the docks via teleporting, killed everybody there and discovered later there was supposed to be some sort of a story relevant to it? That something was supposed to build up to it? So again I felt like I missed out on plot-relevant story payoff. The problem with this current way of doing things isn't the freedom; I love the freedom. The problem is that I feel like I'm in a vacuum, I feel like how I apply that freedom doesn't matter at all.
As for positive stuff, I do like the way sneaking into the castle - teleporting to the scaffolding and sneaking into one of the officials' rooms (the one with the altar and all, and where you hear some plot-related fluff) - was done.