Jay regrets allowing isotropic, because of all the people complaining about losing it. He was happy to have people have it for a while, but not at that price. That is why you can't have nice things.
Then Jay needs to read the tea leaves differently, or not take things personally. We are not upset that we lost Isotropic - we should be grateful Jay (and you) allowed it to begin with (though not as grateful as we are to Doug, who made it work). We should understand that this was a business decision. No problem there.
So let's look at the business side of it. Here we are some 3 years later, with a system that, even when functioning, is not as "nice" as the one that was shut down, despite the application of what we can assume is MANY more resources than Doug ever had (except perhaps brainpower). So I would argue that any "price" that Jay is paying is attached to a bad business decision regarding what would stand in for Isotropic. I would further argue that said price is much higher (in terms of a missed opportunity to expand the Dominion brand and collect the associated revenue) than the monetary value of any company goodwill that RGG lost when Isotropic was shut down.
That "price" continues to escalate, as the lack of progress gets continued attention. It also doesn't help the PR side of the problem to know that Isotropic was used to playtest the latest expansion, because Doug was willing and able to code the cards, yet MF can't even fix their ________ issues (fill in the blank: log-in, lobby capacity, automatch, etc.). Of course, they haven't had much time, and they were starting from scratch, so we shouldn't be overly harsh.