Just a couple things I found irritating.
One, the time it takes mission objectives to respawn is ridiculous. It's actually gotten to the point that I don't want to see other players anywhere near me, because I know that we'll be going for the same activatable object and that I'm probably going to be standing around waiting for quite a while. There's no reason for it, other than to make simple tasks take longer. There is far too much waiting around in this game in general.
Two, at first I thought the combat system was clunky. I now realize that the combat is actually quite fun -- it's the number of enemies, and especially the number of "strongs" which makes getting to any mission area into a chore of most tedious proportions. It ruins the whole flow when I have to kill a hundred things to get to where I'm going, and every fight seems needlessly long. I can't even travel on roads and get from point A to point B without having to stop and fight a bunch of things along the way.
Overall, I love the game. But once I hit level 30 or so, it started to just feel like a really prolonged chore. I already spend 2/3 of the time I'm playing running. Not everything needs to be an exercise of my patience.