If I'm not mistaken "BEM" is a lot like the TNG episode "Justice" so the TAS story isn't far removed from working well enough as a live-action story. Seeing the Bem character disassemble in such a ridiculous manner is a true WTF moment that can jar you out of the story. I certainly felt that way even when I first saw it as a fourteen year old.
It certainly works better in the Alan Dean Foster novelization than in the aired episode. Foster's version has Bem's head crawl along the ground on cilia extending from its neck and his torso walking on its hands, which makes much more sense than having the body parts just hover through the air. Also he could only split into three parts, rather than having the arms separate from the trunk.
But there has been at least one live-action SF show that has used the same premise. This is a spoiler, but in the Buck Rogers in the 25th Century
episode "Journey to Oasis," Mark Lenard played an alien ambassador who could detach his head from his body. I think it was only done once or twice, though.
Another WTF moment (although not quite as bad as "BEM" in my opinion). The idea that the clone Spock had to be oversized to distinguish him from the "real" Spock is silly. All they had to do was draw the clone wearing different clothing.
I don't think it was about distinguishing him. TAS's brief was to do things that couldn't be done in live action, to show striking visuals. Just having clones of Keniclius and Spock would've been too ordinary, so they became giant clones.
But you know as well as I do what STAR TREK was really trying to talk about and the budgetary and technical limitations they were under. So, when you see Alice in Wonderland in SHORE LEAVE, with that kind of understanding, there are connotations ... implications ... and you begin to realize the story they're really trying to tell in a majority of these stories. Whereas with a Fifty Foot Vulcan and BEM's Anatomy are just there as whimsy.
I disagree. Now, those two things are not among the best examples of good ideas in TAS, but the fact that you're cherrypicking them and ignoring better ideas from other episodes just shows that you're trying to justify your prejudice rather than actually evaluate the show fairly.
You mentioned "Shore Leave" -- I give you its sequel, "Once Upon a Planet." Now, "Shore Leave" created the appearance of death and danger, but in the end it turned out to be all just an illusion, nobody had ever been in real danger, and the final revelation was only that advanced aliens like to play too. All rather superficial, really. But in "Once Upon a Planet," the Keeper had actually died, and the planet's central computer, far from being just an obedient mechanism, was revealed to be a sentient artificial life form that considered itself to have been enslaved and that attempted to actually kill the Enterprise
crew in order to liberate itself. That's a much darker, more serious story, certainly with much higher stakes than the original episode, although I grant it does get resolved rather too easily.
Let's look at some other TAS episodes.
"Beyond the Farthest Star": We encounter an alien ship whose crew committed suicide to prevent a malevolent force from escaping into the galaxy. That force gets aboard the ship and threatens and tortures Kirk and Spock to enforce its will.
"Yesteryear": Spock must prevent his own death as a child, and his younger self must face death for the first time and make a decision about the path he will follow in adulthood.
"One of Our Planets Is Missing": The ship must try to prevent the destruction of an entire planet, and we see the anguish of its governor as he deals with the impossible decision of choosing who will be allowed to escape on the few available ships.
"The Lorelei Signal": A race of women needs to lure and kill men in order to stay alive because their own men died and they can't reproduce.
"The Survivor": A spy impersonating a dead man develops real feelings for the man's fiancee.
"The Magicks of Megas-tu": An alien race that suffered extensive persecution, hatred, and violence at human hands seeks justice for those crimes.
"The Slaver Weapon": A deadly enemy seeks to gain control of an ancient weapon of war -- and characters actually die on-camera, something virtually unheard of in 1970s Saturday morning animation.
"The Eye of the Beholder": Much like "The Cage," in that the characters are held prisoner in an alien zoo and must persuade their captors of their right to live free.
"The Jihad": The protagonists must prevent the onset of a holy war that could cause massive death and destruction throughout the known galaxy.
"The Pirates of Orion": Spock is stricken with a terminal disease and Kirk must deal with pirates who have a suicide fetish.
"Albatross": McCoy is arrested for causing a plague that killed hundreds. We see the few survivors of the plague living in horrific conditions.
Look at all that death and danger and suicide and slavery and awful, awful things going on. Sure, due to Saturday morning censorship, the deaths were almost always in the distant past, or threatened and averted; but compare that to a lot of more recent kids' cartoons where the censorship is so strict that the characters aren't even allowed to say
"dead" or "kill" or "die," where the very concept of death is off-limits for discussion. Sure, yeah, there were some bits of whimsy in TAS, but there was also a lot of serious stuff going on, ideas just as adult as anything in TOS.
Heck, there was even a fair amount of sexuality compared to contemporary Saturday morning fare, though very much toned down from TOS: The seductresses of "The Lorelei Signal," the romance between Carter Winston and Anne Nored, Harry Mudd's love potion, an Orion woman wearing only a tiny bikini in "The Time Trap," Lara's flirtation with Kirk in "The Jihad." They did what they could to tell TOS-style stories within the limits of network censorship for Saturday mornings.