I don't think I can really pick one thing. I don't play online Dominion; I haven't much since the Iso days. But the problems I had with Goko that made me not play it are all still around from what I've seen in the new one, along with some new ones:
1. Dragging. There's no excuse for having dragging cards around be a way to say where you want them to go.
2. Screen re-sizing and resolution stuff. Ok so we had this discussion before; some people like full-screen. Well my play style, and general computer usage style, doesn't work with what they offer. I want to be able to drag the corner of my window to change the size of the window, like you can with pretty much every other window that runs under Windows! I don't want to go to the settings and pick a specific size that I'm then stuck using until I'm not in a game.
3. Reconnecting. Even a good program would crash sometimes. There's no reason whatsoever for any server-based implementation of a game to not automatically reconnect you if your computer reboots or your app crashes. Obviously with some sort of timeout. Ok, so my Temporum client doesn't have anything like this. Because it's 100% client-side. But the server-side version that I was working on with someone else? It reconnected you. Without any extra effort in making it do so; it just worked.
4. General slowness. This applies to the speed to start a game, play a game, etc. In Iso you could find, start, and finish a 2 player game extremely quickly. On a powerful board with a strong engine, it could be less than 5 minutes. On the new version, it just takes way too long to play a single game. This is partly due to the matchmaking system, partly due to load times, partly due to animations and such.
I'm sure there's more, but those are the big ones for me.