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
I agree that it would have been better if we had a larger supporting cast. MASH is a good example of having background characters that can step into the spotlight for an episode or two each season. Rizzo, for example had some nice bits in a few episodes but he was never considered a major or even minor regular character, It would have been nice to see more of Kyle for example or Dr. M'Benga. Chekov and Sulu, being on the command track should have been leading a number of landing parties rather than simply tagging along with Kirk & Spock.
When Roddenberry was given the chance to submit a second pilot his story ideas were The Moega Glory and Mudd's Women. Not Trek's worst moment but neither set the tone as well as Peeple's Where No Mas Has Gone Before. Roddenberry was best at the broad strokes. Most other writers were better at telling compelling stories.