I feel like the UI options that are available are not obvious at all. For example, there's that tiny blue arrow you use to flip to the next set of cards in your discard pile when using cards like scavenger or counting house. That should be more obvious. I remember a thread about the annoyance of not knowing what all the knights do when knights are in the kingdom, but there's that small click-able box that displays all the differently named cards in the kingdom.
For me, I didn't find it fair to have to learn the hard way that your cards get played if you click on them through the chat dialog box. I just wanted to focus my cursor on it. It makes sense for the chat to work like that, since it can pop up at any moment in the middle of your turn, but having the chat box be far away from your hand is something I'd personally like to see. I suppose it's not that hard to adapt to the Goko's UI after playing enough games, but it can be really discouraging when that kind of stuff happens the first few times.
I'm thankful that Goko has worked out so many of its old issues, but there's always room for improvement and I think it's important for us, the users of the product and avid players of Dominion, to speak up about implementation problems and counter-intuitive design.