So, what's the best B5 story that could actually work as a single film? I realize the TV films themselves are candidates, but not strong ones, IMHO.

This was a definite improvement over the Byron arc, though the plotting is not as smooth nor the tragic outcome quite as inexorable as one could have hoped. A couple of minor points that always bugged me:

So does Richard actually think well-done burgers are ideal, or did he get "burned" by imperfect temp control in his pretentious wood-fired contraption?

Well, the third and fourth seasons had less of a storytelling straightjacket, though it's true that story beat still cropped up from time to time.

The story template for the first two seasons seemed to require T'Pol to give Archer some good advice, which he would ignore, and then end up in exactly the problem she warned him about.

Indeed. For example, the transporters were "experimental use only" which meant they ended up used only for Deus ex Machina rescues. They lacked the courage to give up on them completely, they just kept the most crutch-like form.

Peter Venkman's World of the Psychic presents: "Undead European White Male Roundtable" causing the ghost of Steve Allen to sue for copyright infringement.

I understand your point, and I'm not trying to pick a fight here. But they're still not part of the same order, even given superficial phenotypic similarities. We see similar results all the time on earth thanks to convergent evolution. Even though Thylacosmilus looks a lot like a Smilodon, it's actually much more…

The Hynerian equivalent of dry humping, obviously. :-)

Scarrans having boobs removes probably one of the least significant biological barriers to crossing with species from another planet. There are thousands of metabolic and developmental pathways that could be fatally incompatible,

I don't imagine many of his concubines felt empowered to say "No, Dominar, that's not my Hynerian clitoris analogue."

And whatever Scarrans are (dragons?). Naj Gil is male, but when he shows off his surgical scar was also get a nipple shot.

Part of the problem is, that having lived in a spaceship completely isolated for 40 years, the episode suggests he's been "preserved" mentally and emotionally in a similar way to her, that he's essentially the same person But in reality he'd be profoundly changed by such an experience (and probably not for the…

Other cliches:
"Let's split up to cover more ground."
Un-sympathizing law enforcement officer (who gets slugged).
This test will tell us lot, too bad we'll never see the results.
Key ally has a family secret that makes turning them trivial.
.

"It’s like if someone’s life turned into a problem out of an ethics textbook."

Spoilers, I guess.

It's a lot worse than the Markab thing, IMHO. While a disease with guaranteed 100% lethality is a stretch, it's not absolutely impossible, and it was used to great effect.

Ryan's always had Wilfred-induced tantrums, but this season he seems especially whiny. It's wearing thin.

What makes it "Marxist" is that the shlemiels getting cockroach bars weren't sufficiently grateful.

It's one of the all time great short stories, but it's a bit thin to base a whole series on.