And, come to think of, this probably is my biggest pet peeve, the one I complain about most: plots where all of the problems stem from characters being totally unwilling to communicate with each other for no reason (or for utterly inane reasons).
I tend to give authors/writers/creators a bit of leeway with this one. I fancy myself to be something of a "keen observer of human character", and almost every problem currently plaguing people stems from some kind of stupid or inane communication breakdown. I have several tedious examples I could share of friends or family members who spent years pointedly not talking to each other because each thought the other was angry at them. And then there's that whole "Palestine" thing...
But there is a line between allowing characters to react stupidly because they are human, and making them act unnecessarily dumb for the sake of a weak plot. Smallville is a good example of both sides of the line. There were some good stories highlighting the parallels between Clark and Lex and their relationships with their fathers (biological or not) in the second and third seasons. After that story arc peaked, though, they turned back into stock "hero" and "villain" cutouts, with much jaw clenching and posturing. (Why couldn't the folks who wrote Spider-man 1 & 2 write Smallville, too?)
Mike "Jurassic Park" Crighton peeves me ....
...by waiting until I get a really great idea for a story, and then churning out one of his formulaic term-paper as fiction shite-burgers with MY idea -- gutted and devoid of any soul -- to feed the pap-swilling masses.
Okay, I may be overstating, and I can't seriously accuse him of plagiarizing me, since I haven't yet written something he could plagiarize. But, I had a really cool idea brewing for a story that revolved around nano-molecular "Smart Dust" (which does exist, BTW), and he went and grunted out "Prey". My story ended up as my rejected <300 word story for the <300 word story contest. (It is here, if you would like to compare them:
http://happyphuntime.blogspot.com/2007/02/ask-dust.html .)
My pet SF peeve is making people of faith, any faith but especially Christians, the bad guys. I'm not a religious fanatic by anyone's standard, but this really gets on my nerves. Not everyone who has their butt in a church on Sunday is a raving, child raping, woman bashing, Luddite, lunatic but you wouldn't know that from reading most SF and much Fantasy.
I have a similar pet peeve regarding books where people of faith, any faith but especially Christians, get to cluck and shake their heads smugly as the rest of us are plunged into some kind of fiery retribution for our lack of faith. My mother, upon hearing my excitement over discovering Asimov, tried to make me read the first Left Behind book. I tried, but after three chapters of chest-beating survivors crying "Why, oh why didn't I listen to all of those wonderful, good-hearted Christians?" I started to detect a note of divine smugness.
In a similar vein, I recently picked up Robert Sawyer's
Calculating God, which uses the story of the first arrival of aliens on Earth to frame a set of arguments in favor of intelligent design. The aliens all believe in the existence of the creator, and the protagonist, a paleontologist, gets to agonize throughout the book over his lack of faith. I kept waiting for him to realize that a) believing the evidence presented by the aliens that "God" exists did not in any way invalidate his beliefs about evolution, and b) evidence of the existence of God does not validate any one particular religion... in fact, it makes the petty differences between them all the more ridiculous. (The book delivers on this, though subtly. And by the way, the Big Scary Villains in the story are economically disadvantaged U.S. Southerners who also happen to be raving, Luddite lunatics. But Sawyer, a Canuck, didn't try to write in the heinous accents... much.)
My point is that there is science fiction out there that deals with religious topics, and some of it actually tries to handle those topics in a way that reflects well on religion. It is hard to find because it is hard to write; and it is hard to write because people of faith already have a (IMHO) fictional universe with set rules and conventions that they don't like writers tampering with.
One last point on this subject: it's not just sci-fi that deals harshly with religious figures. Remember Chaucer? Shakespeare? I seem to recall they took their swipes at the "corrupt priest" from time to time. Piety begs mockery, and false piety begs utter derision.