Roddenberry's worst ideas? Pretty much all of his shows including, to a lesser degree Star Trek. His best idea was to bering in people Coon, Fontana and Jeffries. They are responsible for the best of Trek. Roddenberry could be good in the big ideas but his implementation of the details was usually pretty weak and often laughable. Given a choice of only watching the Non-Roddennberry episodes or the Roddenberry ones I'll take Coon/Fontana/almost anyone else over Gene's.
I am the opposite: The 1st half of S1 is moodier; more like sci-fi shows set in Star Trek, rather than just-another-Trek episode as many became later; more wordsy (I like); featuring more crew going about crew life.
It got too cheerful, almost sappy, as Uhura/Sulu/Checkov got standardized as the-only-other-crewmen-of-note. And the universe got more civilized and starfleetized. YMMV