I've had similar feelings before. But what if they've implemented the only moderation policy that anyone in the history of the internet has discovered to actually work well for fostering discussion among capable people about interesting topics, consistently? The ruleset has evolved slowly over time; they weren't imposed arbitrarily. Each rule was to counteract a specific class of problems plaguing the site. For example, remember the painful discussion about the Airbnb fiasco a few years ago? It stayed on the site for like two days because an angry mob upvoted it so much. (I was a part of it, before later realizing that the story was designed specifically to incite an angry mob.) Etc. There are reasons to penalize certain kinds of content, and sorting it out is a very difficult process. But at least they're trying.
I'm sillysaurus2 because I broke a rule on purpose on my old sillysaurus account. I asked if they'd unban my sillysaurus account, and they were nice enough to unban it. I stuck with sillysaurus2 rather than switching back -- no real reason, just felt like it -- but the point is that they're lenient and they understand that mistakes happen, on both sides of the fence. Contrast that with the policy of, say, /r/AskHistorians: I'm permabanned there for a stupid mistake, and their policy is to give no second chances under any circumstances. So at least these guys are reasonable, yeah?
Yes, it's worrisome that they hold the power of deciding which discussions are penalized. But wouldn't you rather they hold the power rather than some other group? They genuinely believe in merit and good intentions, rather than just using those things as a smoke screen for greed, as some other groups do.
It's not an ideal situation, but it's like democracy: it's the best anyone's thought of so far. But these are just my thoughts, and I'm really interested in hearing yours.