These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Artistic License – Biology: Dr Gediman bizarrely declares that the human reproductive system conferred on the Alien Queen thanks to the experiments has - somehow - made the creature better, when in fact, it appears to drastically reduce the effectiveness of the Xenomorphs; Instead of producing batches of eggs and developing larger numbers of drones, she instead produces one child at a time in a prolonged and clearly painful parallel to human pregnancy; The only discernible advantage is that it now skips the infestation stage that requires other lifeforms. Then again, this may be justified since Gediman is pretty obviously insane.
Complete Monster: Dr. Mason Wren is the head scientist of the covert military operation on the starship the USS Auriga, performing illegal experiments to bring back the Xenomorphs. He clones the deceased Ellen Ripley multiple times to extract the Queen hibernating in her. Most of the clones are born mutated and die agonizing deaths, which he stores for further study. He keeps the second-to-last one alive in constant pain and agony. He persuades General Perez to hire a bunch of space pirates to kidnap deep space travelers while they are still sleeping inside their stasis pods, and then implants them with facehuggers while looking on with smug satisfaction. He is ready to execute all of the pirates on the mere suspicion that one of them might be an infiltrator. When the Xenomorphs escape and they all try to get off the ship, he betrays the others and murders Call as soon as he gets a weapon and leaves everyone else to be killed by the Xenomorphs so he can pilot the ship back to Earth himself. He later takes a hostage whom he threatens to kill in a last attempt to win.
Contested Sequel: though Resurrection still has its fans, thanks primarily to Jeunet's unique visual style, the added humor of Joss Whedon's script, and the presence of cult actors such as Ron Perlman, Dominique Pinion and Michael Wincott.
Cry for the Devil: The Newborn. It was a murderous abomination, but unlike the aliens, shows some emotion, and acts as a naive and childlike creature. And its death was long and agonizing. Even Ripley 8 showed remorse for it - then again, she's kind of its grandmother.
Hilarious in Hindsight: It's now quite easy to see the Betty crew as a dry run for Firefly. The latter may even be Whedon's attempt to show what he really wanted them to be like before the Executive Meddling he's complained so much about.*
Idiot Plot: The entire plot could have been avoided if the people in charge had just thought to invest in a few things like more resilient floors, kept armed guards outside of important cells, not let unreliable mercenaries wander through the important facility and not kept the space station with the dangerous experiments right next to Earth. By that point it makes more sense to assume that they were deliberately trying to wipe out the human race.
Or simply kept titular Aliens in separate cells, so they couldn't kill one of their own to use its acid blod as a way to escape the holding cell.
And of course, the SMALL ARMY of marines, who are supposed to stop the Xenomorphes if they escape, actually RUN AWAY when they do, despite the previous film showing that an outnumbered group of marines could still slaughter much larger numbers of aliens. Really, this was a case of Only the Author Can Save Them Now being done for the villains.
Inferred Holocaust: Ripley saves the day by crashing the xenomorph-filled ship into the Earth causing an impact blast hundreds of miles wide, most likely destroying the biosphere in the process. Nice Job Breaking It, Hero. In the novelization (based on the original script) you learn that Earth was mostly screwed already, which is why one of the characters says, "Earth... what a shithole." The only people still on the planet are the ones that can't afford to leave for one of the colonies.
Les Yay: Ripley and Call. After spending the previous three movies interacting exclusively with males and a surrogate child, Ripley wastes no time in becoming very chummy and touchy very quickly with the cute little android girl whom she first meets when Call attempts to kill her, while Call goes from wanting her as dead as the rest of the aliens to letting Ripley stick her fingers inside of her (not like that, perverts) and confiding her deepest feelings and fears about not being human. From the same movie, there's some Ho Yay between Johner and Vriess, which goes from subtext to text when Johner kisses Vriess at the end of the film because they both lived through all of it.
No Yay: The film features a scene where an Alien is holding Ripley in its arms and carrying her to the Queen's lair. She's not afraid of it, and embraces the creature. The sequence is shot and framed as if it were a love scene. Now remember that the Aliens are an Always Chaotic Evil race of utterly inhuman alien monsters that face-rape people and have killed almost everyone that Ripley ever knew or loved.
Call. Of course, that's because she's Newt, only older and a robot.
To some the Newborn is this, stealing the scene that should be of the xenomorphs and being introduced in the last 30 seconds. though many fans see it as The Woobie, others think it utterly fails at being sympathetic: xenomorphs may be more dangerous, but they kill only when they need to, and favor a cold efficency over wanton brutality. The Newborn on the other hand, is utterly psychotic and kills for the sake of it, and many think that its big puppy dog eyes are simply a facade to lower its victims's guard.
Too Cool to Live: The gravely-voiced head of the Betty crew Captain Elgyn is portrayed as a careless space pirate and ladies man. He's also the first of them to die in a rather sudden and painful death.
Special Effects Failure: The special effects quality takes a major nosedive from the previous three films, mostly due to the film's whole-hearted embrace of CGI for nearly all the special effects outside of the individual Xenomorphs. Granted, even back in 1997 there were many films that made decent use of the technology, but the CGI in this film somehow manages to be vastly worse than what the likes of Babylon 5 and Star Trek: Voyager were doing on television at the same time (Most of which were done by the guys who would work on Ice Age several years later). The actual Xenomorph effects are at least decent for the most part, until the Newborn shows up (granted, most of the problems with that thing were with its very concept. But the execution didn't really help at all). The kicker is the Conspicuous CGI hand grenade that rolls down into an escape pod. Dodgy CGI on complex extraterrestrials is one thing, having a close-up on a poorly-rendered rolling grenade is another.
Wheelchair Woobie: Vriess. Complete with a scene where Johner throws a knife into one of his numb legs, just to be an ass!