I'd definitely class City on the Edge of Forever,
Stupid massive plot hole - why didn't Kirk just tale Edith to the future with him? Same result. She didn't have to die at all and Kirk could have lived happily ever after. If it's about keeping the timeline exactly as it was to the last detail, they'd already failed when the bum was toasted by McCoy's phaser.
The Romulan ship is repeatedly said to not have warp drive, which is embarrasingly awful science - they'd never have a hope in hell against an FTL ship like the Enterprise. The Enterprise's phasers also mysteriously look, sound and act exactly like photon torpedoes.
An it-was-all-a-dream episode where Picard learned to play the flute.
and In The Pale Moonlight
Totally undermines Star Trek. When the good guys are no better than the villains, there is no optimistic future. Also, that "It's a FAAAAKE!" was probably the cheesiest corniest thing in modern Trek.
as smart TV. Similarly I'd call Wrath of Khan
Ceti Alpha VI exploded. Erm, why? How? Starfleet somehow missed this and mistook Ceti Alpha V for VI? There is no chance that could happen. An idiot would notice the planets were different to how they were 15 years earlier.
Khan doesn't grasp the fact that space is three dimensional - which completely destroys any credibility he may have had. Super intelligent? I think you'd struggle to find a non-Augmented someone who doesn't realize space is 3D.
And Genesis. Makes no sense in terms of Trek technology, in terms of real science, in terms of story.
Where a Klingon faps to Shakespeare, the Klingons have a ship that can fire while cloaked (a technology they somehow never try again), where the Enterprise crew are treated awfully (Uhura doesn't know Klingon? McCoy doesn't know Klingon anatomy? Kirk's a racist?), and where an exploding moon in Klingon space somehow hits and damages a ship in Federation space but nothing else. The original ending had the Next Generation crew take over from Kirk's - until someone reminded them that the shows are separated by 80 years.
Oh, and the Klingon/Federation peace was pre-undermined by "Yesterday's Enterprise" which showed the real peace stemmed from an incident 22 years prior to TNG.
Making out that Star Trek has always been stupid just isn't a valid excuse.
I love Trek and I enjoyed all the episodes I just tore apart - but I like it for what it really is, not for what the 80's/90's hype said it was. It doesn't fit on the pedestal you're putting it on. You may dislike the new movies and their direction, but they're not fundamentally "dumber" than what came before. Just louder, more intense and less pretentious.