I think the biggest reason I don't play on goko is the interface. On my turn, I pretty much know what's going on. However, on my opponents turn (especially against AI) all I see is a lots of cards moving around the board and then its my turn again. I look at the log to figure out what my opponent did, and it takes me a full minute to learn that my opponent played an ironmonger and a witch and bought a gold. The logs really need some formatting.
Additionally, whenever some plays militia, I always thinks it's my turn so I try to play my witch. That ends badly. Maybe a warning should be implemented if you're discarding something besides victory cards, curses, or coppers.
These are also my problems with it. It's all UI.
I have animations on fast, because I don't want to waste time and be annoyed by watching the animations. But that means I have to open and close the log every damn turn. I think you'd have to have animations on slow and pay super-close attention to avoid that. Or just not care about what the other players do on your turn. I'm sure lots of casual players don't care, but I play competitively.
That log is way more difficult to read than on isotropic. It's just a wall of text with no color or formating, and lots of unnecessary repetition. Talk about a non-graphical interface! Scrolling up is also incredibly wonky. I find myself using the scroll wheel on my mouse, which doesn't work of course. So you have to grab that scrollbar. But it seems when you first click the scrollbar, you're stuck dragging it, even the next time you open the log? I think you have to click again to un-grab?? Something non-intuitive anyway. Really really annoying stuff.
When you have to click several cards, after each card, the others get a little "activation animation", which is NOT any faster when you set animation to fast. Selecting several cards should be just that: selecting - like on iso. You check the cards, THEN do the thing, discard or whatever. This would be much more convenient, and would save you from accidentally discarding your Witch to a Militia attack because you think it's your turn. Also, trashing each card in turn (with e.g. Chapel) is wrong rules-wise: You trash them all at once. Even if this works correctly on Goko now, it gives the wrong impression to the player: It seems each card is trashed after the other.
More about selecing cards: I played with Schemes (lots of them), and a more-or-less self-drawing deck. With lots of cards in play, I had to select those card slivers. They were not grouped at all. It was impossible to see what I was selecting: the only thing that identified them was a sliver of the card art at the side. When actually selecting a card to Scheme, it moved to the front of the huge line of cards for some reason, but was otherwise not marked. If I wanted to look at a card sliver (to see what card i was), I could do that by pulling it out I think. This did not Scheme it (which is good), but it DID move to the front of the line! So which cards had I actually Schemed? Impossible to tell. A nightmare. Isotropic does this well.
Intuitiveness and chat: When opening the chat window, I find myself clicking in the textbox to start typing there. This works horribly, as I could easily click on a card below the textbox. So even if this is HTML-based, they are using "proprietary" textboxes that work differently than everybody is used to on the web. You can't use Home or End or arrow keys to edit what you write. A typing mistake at the beginning means you have to delete everything you wrote and start over, or just post it anyway. Why..??