Here are my reasons at the moment (not particularly in any order):
1. Cards - I have access to all the cards prior to DA on Isotropic for free. All things considered $45 for all the cards is a pretty good deal (particularly as I haven't bought them IRL yet), but for now Isotropic is a better option as I am learning the game.
2. More game options - I am still pretty new to Dominion so I am still working on learning the different cards and how to play them in different situations. On Isotropic I can limit or bias automatch selections based on expansion and so far this isn't an option on Goko. So when I played some Goko I would be thrown into a few games full of Dark Ages cards and/or with a lot of cards I'm unfamiliar with, which would make the games a lot harder for me and I can't really ease my way into the different decks like I can on Isotropic. I don't really choose to use the point tracker or veto on Isotropic (I usually automatch with don't care on both settings, so I'm willing to play with them, but don't by default) and some options like this would be nice to have available on Goko.
3. No automatch / smaller userbase - This is obviously a common complaint. Often there aren't many open games at any one point and even if you create one there isn't really any assurance that the player you play will be around your skill level (though of course you can kick them out, it just seems a bit inefficient). The userbase will obviously increase once Goko leaves the beta phase and Isotropic is ended, but everyone will not necessarily migrate over, the amount of cards people have will be variable rather than unified, and there still is not an effective way to match similar-skilled players.
4. User Interface - First, one of my main problems is the in-game chat log. I personally don't really go back and look at my game logs, but that also seems to be an issue. However, I do want to know what is happening in the game and sometimes its really hard to get that on Goko. I want to be able to see what my opponent played and did and sometimes its difficult to tell with the animations either being too fast or too slow. The Goko Log parser looks like its great, though I haven't had the chance to try it yet, but I do to some extent still have a problem that some people may have access to that while others might not, giving the group using it an advantage (even if its the same information), and how its something that should really be implemented into the game itself. Second, it would be nice to have some sort of safety against misclicks like Isotropic has. Sometimes I get impatient and wind up misclicking, I have been Militia'd and thinking it was my turn I have accidently discarded a Witch (secondary complaint, though there are color differences in the aura around the cards from attacks and your turn, it still is somewhat subtle and easy to misclick with) which could be helped by some sort of confirmation quickly, and the other cases that Isotropic seems to defend against. Thirdly, hand organization. Fourth, those avatars?
5. Unreliability - I haven't played Goko as much recently and I have heard that it has been getting better and more reliable (though there are still some complaints of crashing), but I had some trouble with crashing if I had more than a few other windows open in Chrome other than Goko. I saw that there now is rejoining upon disconnecting, but I haven't tested it yet. I see that as a positive step though.
6. Rankings - The rankings on Isotropic seem much more straightforward and there has seemed to be less variation for me in the rankings on Isotropic than on Goko, though part of that may be that Iso is updated daily rather than after every game like Goko. Though the systems are supposed to be similar I feel like sometimes there are ridiculous point swings for me on Goko. I think that I've had some games on Goko that I have won yet lost points (or maybe gained a very, very small amount of points) and I am no expert in the game, just okay and sometimes playing the only game I can really get, which goes back to the smaller userbase and lack of automatch. Its also much harder to understand really where I stand with the rankings. Yes, there is a leaderboard, but thats a lot more relative and the levels on Isotropic, though not all-encompassing, give a more discrete idea of position.
7. Distrust of the company - There have been a lot of complaints about Goko's communication and relation to the community, and though I haven't been around for a lot of it, that is what I have seen so far. The failed beta launch being the premier example. Past that, there seems to often be a lack of communication by Goko with the community and I don't feel totally confident in the extent that they are listening to our concerns. This has been particularly prescient following the departure of a few staff from the company, particularly trisha, who seemed to be more involved in the community. To be fair, they have held some Q&A's and seem to be working on some of the things that this community has looked at. I also in principle dislike secondary currency units instead of just paying in straight dollars (both here on Goko and even things like Xbox live marketplace) and don't like how they just recently upped some of the prices as Alchemy came out, though they do have the right to set prices where they see fit. Some of the problems hurt my confidence in general about the product and my willingness to put down the money for the cards in a virtual format when the platform may or may not be there in the future.
Overall, I do plan to play more on Goko and make a switch when it leaves beta. However, I still have some misgivings and right now I feel like isotropic is simpler and preferable to me at the moment. I will probably wait a bit, but will likely try and buy all the cards at some point, maybe once I gain more confidence in Goko overall.