Is the issue with the fact that they did a puppet episode at all, or is the issue with the episode's execution? I love the idea of a puppet Star Trek episode but had some issues with how it was done. Generally I enjoyed it, though.
Star Trek writer Keith DeCandidio mocks fans for being concerned about Star Trek becoming ridiculous with puppets:
"I must confess to amusement—or is it bemusement?—at all the online fulminating about doing a puppet/Muppet episode, as if that soils the purity of Star Trek. The same Star Trek that has (checks notes) the captain riding the first officer like a horse, the Enterprise encountering Abraham Lincoln floating in space and a giant space amoeba and a doomsday machine that looks like a cornucopia that lost a bar fight, the captain having hundreds of tribbles dumped on his head, the ship’s doctor having green smoke sex with a candle, the Enterprise visiting the Nazi planet and the Roman Empire planet and the Greek god planet and the gangster planet and the Aryan sex addict planet, Voyager creating a warp drive that turns you into a horny salamander, the captain’s dog peeing on a planet thus contaminating its biosphere, the crew playing a game that is like Jenga but without the deep intellectualism, the crew being 'de-evolved' (more than once!), the security chief being killed by a sadistic oil slick, the Enterprise ferrying fish people and space hippies, etc."
Despite Star Trek having a lot of quirky episodes, didn't it at least try to take itself seriously before?