Personally, I can only take a certain amount of meta while still being engaged in the story. When characters repeatedly tell you that what's happening isn't real, but just a story, you inevitably lose all the stakes. Really, this is something that can happen in any art form, if you keep deconstructing it, you eventually end up with nothing.
Of course, being what it is, this episode brings up this very point. Rick says something along the lines of "meta works in a comment here or there, but if you base a whole story on it, it breaks down". When characters blatantly point out the problems with the story they're in, at best it comes across as self-deprecating, and at worst, as obnoxious and irritating. What it doesn't do, is fixing the problem. It's just the writer saying, "I know this is flawed but I'm doing it anyway", or maybe "I know what you're going to dislike about this, so I'm saying it first to get ahead of you".
At its best, Rick and Morty gives you funny jokes and an engaging story, this had one of those things. The jokes carry the episode and make it worth watching, (the Self-Referential Six was a personal highlight) even though it's very hard to care about anything that is happening.