Supposedly the departing Gene Coon intended it as a comedy along the lines of "Tribbles". Fred Freiberger wanted it played straight and Coon became "Lee Cronin" for his writing credit.
The earlier version barely featured Nimoy. Spock's body was left back in sickbay - it would have been a useful episode if the actor had required a few days' leave from the set. The only reason we see zombiefied Spock is because they rejigged the script to give Nimoy a presence in the planetary scenes. IIRC, his inert body gets left behind in the Blish adaptation.
For me, the most embarrassingly bad episode was "Plato's Stepchildren". My Dad once sat watching that episode throughout, with me only knowing it via the Blish adaptation. Don't remind me of the horsey stuff.
The 'Spock's Brain was meant to be a Gene Coon comedy' is just a myth. There wasn't anything funny about Coon's early-draft script, it was just an uncharacteristically terrible script from Trek's best writer. The only bit of humour in the first draft was the mandatory Spock/Bones insult trading session just before the credits.
Shatner certainly was in comedy mode though that week

The story goes that seasons 2 and 3 were opened with Spock episodes to cash in on his popularity. Fair enough, but you have to wonder why they didn't go with The Enterprise Incident for Season 3's opener. Plenty of Spock in that one, too.
I agree that Plato's Stepchildren is among the worst of the worst, sitting alongside Gamesters, and And the Children...IMO.