Brain isn't that bad, it's just not all that good.
It was TV. Not a medium known for its depth at the time, or now for that matter.
What it is, is Star Trek. Trek did (and does) good and bad episodes, and they're all Star Trek. Even the movies do the exact same thing as all the series have done. Good episodes, and not so good ones. They're all Star Trek, so they're all good.
Of all the TOS episodes, the only one that I really truly dislike is The Alternative Factor. As for Spock's Brain, I have come to appreciate it over the years, is fun in the same way that the Batman TV series was fun.