This is the obligatory mention of FOX and Executive Meddling.

Wasn't nearly enough of Firefly.

What’s with the lack of Asians in a supposedly China-dominated ‘Verse?

We never got to see the crappy town where Wash was a hero.

How they never explained what the hell Book's deal was.

The Big Damn Spoiler ( death of Wash) in the Big Damn Movie. The Mal/Zoe shippers were probably overjoyed, though...

• Honestly though, knowing Whedon's work, this troper think if the show had gone on as long as Buffy, we'd likely have lost several crew members by the end. Though Kaylee's my favourite, I think she either would have eventually become a victim of Kill The Cutie or Break The Cutie. Heck, pretty much everyone except River would have had a realistic chance of getting killed.
• I can see Mal and Zoe being the last ones left, trying to save River and Simon who have something that can hurt the Alliance on at least the scale of the end of Serenity.

The Reavers always bothered me. If they are so insanely violent, consumed with killing and torture and beyond all reason, and their ships fly without "containment" (very dangerous, apparently), who flies the ship? Somehow, it seems much too calm and rational. Also- how is it they don't attack each other? They don't seem like the type to think long enough to collaborate.

"The Message" has always been frought with Fridge Logic for me. First off, they said that Tracey's own organs were removed to make room for the transplant organs he was smuggling. What happens at the rendevous, when Tracey gives up the smuggled organs and his own guts are halfway across the 'verse from him?

And that doesn't even touch the fact that noone bothered to try to explain the plan to Tracey after he decided they were going to abandon him to the Fed, which would have cleaned the whole thing right up.

Simon rescuing his sister himself in the Big Damn Movie bugs me intensely, for two reasons. A) He was never an action guy, so to see him leaping around like some kind of superhero is really disconcerting, and B) things are revealed to him prior to/during the rescue that he then doesn't seem to know about in the TV show. If he was talking to them about what they were doing to her brain, why didn't he know they'd been doing things to her brain until Ariel? and why doesn't he know why they were doing it? He was straight out told both in the rescue.

River didn't go barefoot nearly enough.

The random, minute-plus long sex scenes thrown in, all of which could be excised with no effect on the understandability of the plot. We get that sex is a natural part of life. They don't have to pass the ten second mark, actually, to send that message, so they're padding or fanservice.

Either way, it's awkward to show it to a parent or friend who would like the show otherwise, but is the tiniest bit uptight about it. (And no, they don't need their horizons broadened, they get that it's natural, too - they're just vaguely uncomfortable talking about it. Personal limits.)

I find it hard to accept that a single solar system could support such a large number of habitable planets and moons, even counting "yeah but we terraformed it" as "habitable."

Too far from a System's star, or too close to it, and life as we know it can't exist regardless of any terraforming. Especially if you want familiar lifeforms, above ground and not encased in controlled life-domes or something. for example, you can't terraform even Venus or Jupiter's moons and end up with cows munching on grass.

• Aren't there supposed to be several stars in the system?

Mal makes it clear that Simon and River are part of his crew. He nearly kills Jayne for trying to sell them out, explicitly for that reason. So his behavior at the beginning of the movie, tossing Simon and River off the ship for Simon's minor infraction of punching the captain and mouthing off, seems a bit out of character.